diff --git a/IPython/core/alias.py b/IPython/core/alias.py
index 0905c19..0140b2e 100644
--- a/IPython/core/alias.py
+++ b/IPython/core/alias.py
@@ -20,17 +20,15 @@ Authors:
 # Imports
 #-----------------------------------------------------------------------------
 
-import __builtin__
-import keyword
 import os
 import re
 import sys
 
 from IPython.config.configurable import Configurable
-from IPython.core.splitinput import split_user_input
+from IPython.core.error import UsageError
 
 from IPython.utils.traitlets import List, Instance
-from IPython.utils.warn import warn, error
+from IPython.utils.warn import error
 
 #-----------------------------------------------------------------------------
 # Utilities
@@ -104,6 +102,70 @@ class AliasError(Exception):
 class InvalidAliasError(AliasError):
     pass
 
+class Alias(object):
+    """Callable object storing the details of one alias.
+
+    Instances are registered as magic functions to allow use of aliases.
+    """
+
+    # Prepare blacklist
+    blacklist = {'cd','popd','pushd','dhist','alias','unalias'}
+
+    def __init__(self, shell, name, cmd):
+        self.shell = shell
+        self.name = name
+        self.cmd = cmd
+        self.nargs = self.validate()
+
+    def validate(self):
+        """Validate the alias, and return the number of arguments."""
+        if self.name in self.blacklist:
+            raise InvalidAliasError("The name %s can't be aliased "
+                                    "because it is a keyword or builtin." % self.name)
+        try:
+            caller = self.shell.magics_manager.magics['line'][self.name]
+        except KeyError:
+            pass
+        else:
+            if not isinstance(caller, Alias):
+                raise InvalidAliasError("The name %s can't be aliased "
+                                        "because it is another magic command." % self.name)
+
+        if not (isinstance(self.cmd, basestring)):
+            raise InvalidAliasError("An alias command must be a string, "
+                                    "got: %r" % self.cmd)
+
+        nargs = self.cmd.count('%s')
+
+        if (nargs > 0) and (self.cmd.find('%l') >= 0):
+            raise InvalidAliasError('The %s and %l specifiers are mutually '
+                                    'exclusive in alias definitions.')
+
+        return nargs
+
+    def __repr__(self):
+        return "<alias {} for {!r}>".format(self.name, self.cmd)
+
+    def __call__(self, rest=''):
+        cmd = self.cmd
+        nargs = self.nargs
+        # Expand the %l special to be the user's input line
+        if cmd.find('%l') >= 0:
+            cmd = cmd.replace('%l', rest)
+            rest = ''
+        if nargs==0:
+            # Simple, argument-less aliases
+            cmd = '%s %s' % (cmd, rest)
+        else:
+            # Handle aliases with positional arguments
+            args = rest.split(None, nargs)
+            if len(args) < nargs:
+                raise UsageError('Alias <%s> requires %s arguments, %s given.' %
+                      (self.name, nargs, len(args)))
+            cmd = '%s %s' % (cmd % tuple(args[:nargs]),' '.join(args[nargs:]))
+
+        self.shell.system(cmd)
+
 #-----------------------------------------------------------------------------
 # Main AliasManager class
 #-----------------------------------------------------------------------------
@@ -116,35 +178,19 @@ class AliasManager(Configurable):
 
     def __init__(self, shell=None, **kwargs):
         super(AliasManager, self).__init__(shell=shell, **kwargs)
-        self.alias_table = {}
-        self.exclude_aliases()
+        # For convenient access
+        self.linemagics = self.shell.magics_manager.magics['line']
         self.init_aliases()
 
-    def __contains__(self, name):
-        return name in self.alias_table
-
-    @property
-    def aliases(self):
-        return [(item[0], item[1][1]) for item in self.alias_table.iteritems()]
-
-    def exclude_aliases(self):
-        # set of things NOT to alias (keywords, builtins and some magics)
-        no_alias = set(['cd','popd','pushd','dhist','alias','unalias'])
-        no_alias.update(set(keyword.kwlist))
-        no_alias.update(set(__builtin__.__dict__.keys()))
-        self.no_alias = no_alias
-
     def init_aliases(self):
-        # Load default aliases
-        for name, cmd in self.default_aliases:
-            self.soft_define_alias(name, cmd)
-
-        # Load user aliases
-        for name, cmd in self.user_aliases:
+        # Load default & user aliases
+        for name, cmd in self.default_aliases + self.user_aliases:
             self.soft_define_alias(name, cmd)
 
-    def clear_aliases(self):
-        self.alias_table.clear()
+    @property
+    def aliases(self):
+        return [(n, func.cmd) for (n, func) in self.linemagics.items()
+                            if isinstance(func, Alias)]
 
     def soft_define_alias(self, name, cmd):
         """Define an alias, but don't raise on an AliasError."""
@@ -159,104 +205,33 @@ class AliasManager(Configurable):
         This will raise an :exc:`AliasError` if there are validation
         problems.
         """
-        nargs = self.validate_alias(name, cmd)
-        self.alias_table[name] = (nargs, cmd)
+        caller = Alias(shell=self.shell, name=name, cmd=cmd)
+        self.shell.magics_manager.register_function(caller, magic_kind='line',
+                                                    magic_name=name)
 
-    def undefine_alias(self, name):
-        if name in self.alias_table:
-            del self.alias_table[name]
+    def get_alias(self, name):
+        """Return an alias, or None if no alias by that name exists."""
+        aname = self.linemagics.get(name, None)
+        return aname if isinstance(aname, Alias) else None
 
-    def validate_alias(self, name, cmd):
-        """Validate an alias and return the its number of arguments."""
-        if name in self.no_alias:
-            raise InvalidAliasError("The name %s can't be aliased "
-                                    "because it is a keyword or builtin." % name)
-        if not (isinstance(cmd, basestring)):
-            raise InvalidAliasError("An alias command must be a string, "
-                                    "got: %r" % cmd)
-        nargs = cmd.count('%s')
-        if nargs>0 and cmd.find('%l')>=0:
-            raise InvalidAliasError('The %s and %l specifiers are mutually '
-                                    'exclusive in alias definitions.')
-        return nargs
+    def is_alias(self, name):
+        """Return whether or not a given name has been defined as an alias"""
+        return self.get_alias(name) is not None
 
-    def call_alias(self, alias, rest=''):
-        """Call an alias given its name and the rest of the line."""
-        cmd = self.transform_alias(alias, rest)
-        try:
-            self.shell.system(cmd)
-        except:
-            self.shell.showtraceback()
-
-    def transform_alias(self, alias,rest=''):
-        """Transform alias to system command string."""
-        nargs, cmd = self.alias_table[alias]
-
-        if ' ' in cmd and os.path.isfile(cmd):
-            cmd = '"%s"' % cmd
-
-        # Expand the %l special to be the user's input line
-        if cmd.find('%l') >= 0:
-            cmd = cmd.replace('%l', rest)
-            rest = ''
-        if nargs==0:
-            # Simple, argument-less aliases
-            cmd = '%s %s' % (cmd, rest)
+    def undefine_alias(self, name):
+        if self.is_alias(name):
+            del self.linemagics[name]
         else:
-            # Handle aliases with positional arguments
-            args = rest.split(None, nargs)
-            if len(args) < nargs:
-                raise AliasError('Alias <%s> requires %s arguments, %s given.' %
-                      (alias, nargs, len(args)))
-            cmd = '%s %s' % (cmd % tuple(args[:nargs]),' '.join(args[nargs:]))
-        return cmd
-
-    def expand_alias(self, line):
-        """ Expand an alias in the command line
+            raise ValueError('%s is not an alias' % name)
 
-        Returns the provided command line, possibly with the first word
-        (command) translated according to alias expansion rules.
-
-        [ipython]|16> _ip.expand_aliases("np myfile.txt")
-                 <16> 'q:/opt/np/notepad++.exe myfile.txt'
-        """
-
-        pre,_,fn,rest = split_user_input(line)
-        res = pre + self.expand_aliases(fn, rest)
-        return res
-
-    def expand_aliases(self, fn, rest):
-        """Expand multiple levels of aliases:
-
-        if:
-
-        alias foo bar /tmp
-        alias baz foo
-
-        then:
-
-        baz huhhahhei -> bar /tmp huhhahhei
-        """
-        line = fn + " " + rest
-
-        done = set()
-        while 1:
-            pre,_,fn,rest = split_user_input(line, shell_line_split)
-            if fn in self.alias_table:
-                if fn in done:
-                    warn("Cyclic alias definition, repeated '%s'" % fn)
-                    return ""
-                done.add(fn)
-
-                l2 = self.transform_alias(fn, rest)
-                if l2 == line:
-                    break
-                # ls -> ls -F should not recurse forever
-                if l2.split(None,1)[0] == line.split(None,1)[0]:
-                    line = l2
-                    break
-                line = l2
-            else:
-                break
-
-        return line
+    def clear_aliases(self):
+        for name, cmd in self.aliases:
+            self.undefine_alias(name)
+
+    def retrieve_alias(self, name):
+        """Retrieve the command to which an alias expands."""
+        caller = self.get_alias(name)
+        if caller:
+            return caller.cmd
+        else:
+            raise ValueError('%s is not an alias' % name)
diff --git a/IPython/core/completer.py b/IPython/core/completer.py
index 642bdae..ee07b26 100644
--- a/IPython/core/completer.py
+++ b/IPython/core/completer.py
@@ -431,8 +431,7 @@ class IPCompleter(Completer):
     )
 
     def __init__(self, shell=None, namespace=None, global_namespace=None,
-                 alias_table=None, use_readline=True,
-                 config=None, **kwargs):
+                 use_readline=True, config=None, **kwargs):
         """IPCompleter() -> completer
 
         Return a completer object suitable for use by the readline library
@@ -450,9 +449,6 @@ class IPCompleter(Completer):
           handle cases (such as IPython embedded inside functions) where
           both Python scopes are visible.
 
-        - If alias_table is supplied, it should be a dictionary of aliases
-          to complete.
-
         use_readline : bool, optional
           If true, use the readline library.  This completer can still function
           without readline, though in that case callers must provide some extra
@@ -476,9 +472,6 @@ class IPCompleter(Completer):
         # List where completion matches will be stored
         self.matches = []
         self.shell = shell
-        if alias_table is None:
-            alias_table = {}
-        self.alias_table = alias_table
         # Regexp to split filenames with spaces in them
         self.space_name_re = re.compile(r'([^\\] )')
         # Hold a local ref. to glob.glob for speed
@@ -505,7 +498,6 @@ class IPCompleter(Completer):
         self.matchers = [self.python_matches,
                          self.file_matches,
                          self.magic_matches,
-                         self.alias_matches,
                          self.python_func_kw_matches,
                          ]
 
@@ -628,22 +620,6 @@ class IPCompleter(Completer):
             comp += [ pre+m for m in line_magics if m.startswith(bare_text)]
         return comp
 
-    def alias_matches(self, text):
-        """Match internal system aliases"""
-        #print 'Completer->alias_matches:',text,'lb',self.text_until_cursor # dbg
-
-        # if we are not in the first 'item', alias matching
-        # doesn't make sense - unless we are starting with 'sudo' command.
-        main_text = self.text_until_cursor.lstrip()
-        if ' ' in main_text and not main_text.startswith('sudo'):
-            return []
-        text = os.path.expanduser(text)
-        aliases =  self.alias_table.keys()
-        if text == '':
-            return aliases
-        else:
-            return [a for a in aliases if a.startswith(text)]
-
     def python_matches(self,text):
         """Match attributes or global python names"""
         
diff --git a/IPython/core/interactiveshell.py b/IPython/core/interactiveshell.py
index 5c9a7a4..75f064d 100644
--- a/IPython/core/interactiveshell.py
+++ b/IPython/core/interactiveshell.py
@@ -470,7 +470,6 @@ class InteractiveShell(SingletonConfigurable):
         # because it and init_io have to come after init_readline.
         self.init_user_ns()
         self.init_logger()
-        self.init_alias()
         self.init_builtins()
 
         # The following was in post_config_initialization
@@ -502,6 +501,7 @@ class InteractiveShell(SingletonConfigurable):
         self.init_displayhook()
         self.init_latextool()
         self.init_magics()
+        self.init_alias()
         self.init_logstart()
         self.init_pdb()
         self.init_extension_manager()
@@ -1363,9 +1363,7 @@ class InteractiveShell(SingletonConfigurable):
             namespaces = [ ('Interactive', self.user_ns),
                            ('Interactive (global)', self.user_global_ns),
                            ('Python builtin', builtin_mod.__dict__),
-                           ('Alias', self.alias_manager.alias_table),
                            ]
-            alias_ns = self.alias_manager.alias_table
 
         # initialize results to 'null'
         found = False; obj = None;  ospace = None;  ds = None;
@@ -1404,8 +1402,6 @@ class InteractiveShell(SingletonConfigurable):
                     # If we finish the for loop (no break), we got all members
                     found = True
                     ospace = nsname
-                    if ns == alias_ns:
-                        isalias = True
                     break  # namespace loop
 
         # Try to see if it's magic
@@ -1940,7 +1936,6 @@ class InteractiveShell(SingletonConfigurable):
         self.Completer = IPCompleter(shell=self,
                                      namespace=self.user_ns,
                                      global_namespace=self.user_global_ns,
-                                     alias_table=self.alias_manager.alias_table,
                                      use_readline=self.has_readline,
                                      parent=self,
                                      )
@@ -2305,7 +2300,6 @@ class InteractiveShell(SingletonConfigurable):
     def init_alias(self):
         self.alias_manager = AliasManager(shell=self, parent=self)
         self.configurables.append(self.alias_manager)
-        self.ns_table['alias'] = self.alias_manager.alias_table,
 
     #-------------------------------------------------------------------------
     # Things related to extensions
diff --git a/IPython/core/magics/osm.py b/IPython/core/magics/osm.py
index 71f0035..3cfc0f0 100644
--- a/IPython/core/magics/osm.py
+++ b/IPython/core/magics/osm.py
@@ -26,6 +26,7 @@ from pprint import pformat
 from IPython.core import magic_arguments
 from IPython.core import oinspect
 from IPython.core import page
+from IPython.core.alias import AliasError, Alias
 from IPython.core.error import UsageError
 from IPython.core.magic import  (
     Magics, compress_dhist, magics_class, line_magic, cell_magic, line_cell_magic
@@ -113,10 +114,14 @@ class OSMagics(Magics):
         # Now try to define a new one
         try:
             alias,cmd = par.split(None, 1)
-        except:
-            print oinspect.getdoc(self.alias)
-        else:
-            self.shell.alias_manager.soft_define_alias(alias, cmd)
+        except TypeError:
+            print(oinspect.getdoc(self.alias))
+            return
+        
+        try:
+            self.shell.alias_manager.define_alias(alias, cmd)
+        except AliasError as e:
+            print(e)
     # end magic_alias
 
     @line_magic
@@ -124,7 +129,12 @@ class OSMagics(Magics):
         """Remove an alias"""
 
         aname = parameter_s.strip()
-        self.shell.alias_manager.undefine_alias(aname)
+        try:
+            self.shell.alias_manager.undefine_alias(aname)
+        except ValueError as e:
+            print(e)
+            return
+        
         stored = self.shell.db.get('stored_aliases', {} )
         if aname in stored:
             print "Removing %stored alias",aname
@@ -182,7 +192,7 @@ class OSMagics(Magics):
                             try:
                                 # Removes dots from the name since ipython
                                 # will assume names with dots to be python.
-                                if ff not in self.shell.alias_manager:
+                                if not self.shell.alias_manager.is_alias(ff):
                                     self.shell.alias_manager.define_alias(
                                         ff.replace('.',''), ff)
                             except InvalidAliasError:
@@ -190,7 +200,7 @@ class OSMagics(Magics):
                             else:
                                 syscmdlist.append(ff)
             else:
-                no_alias = self.shell.alias_manager.no_alias
+                no_alias = Alias.blacklist
                 for pdir in path:
                     os.chdir(pdir)
                     for ff in os.listdir(pdir):
diff --git a/IPython/core/prefilter.py b/IPython/core/prefilter.py
index 49204bf..15aba20 100644
--- a/IPython/core/prefilter.py
+++ b/IPython/core/prefilter.py
@@ -488,22 +488,6 @@ class AutoMagicChecker(PrefilterChecker):
         return self.prefilter_manager.get_handler_by_name('magic')
 
 
-class AliasChecker(PrefilterChecker):
-
-    priority = Integer(800, config=True)
-
-    def check(self, line_info):
-        "Check if the initital identifier on the line is an alias."
-        # Note: aliases can not contain '.'
-        head = line_info.ifun.split('.',1)[0]
-        if line_info.ifun not in self.shell.alias_manager \
-               or head not in self.shell.alias_manager \
-               or is_shadowed(head, self.shell):
-            return None
-
-        return self.prefilter_manager.get_handler_by_name('alias')
-
-
 class PythonOpsChecker(PrefilterChecker):
 
     priority = Integer(900, config=True)
@@ -591,20 +575,6 @@ class PrefilterHandler(Configurable):
         return "<%s(name=%s)>" % (self.__class__.__name__, self.handler_name)
 
 
-class AliasHandler(PrefilterHandler):
-
-    handler_name = Unicode('alias')
-
-    def handle(self, line_info):
-        """Handle alias input lines. """
-        transformed = self.shell.alias_manager.expand_aliases(line_info.ifun,line_info.the_rest)
-        # pre is needed, because it carries the leading whitespace.  Otherwise
-        # aliases won't work in indented sections.
-        line_out = '%sget_ipython().system(%r)' % (line_info.pre_whitespace, transformed)
-
-        return line_out
-
-
 class MacroHandler(PrefilterHandler):
     handler_name = Unicode("macro")
 
@@ -730,14 +700,12 @@ _default_checkers = [
     IPyAutocallChecker,
     AssignmentChecker,
     AutoMagicChecker,
-    AliasChecker,
     PythonOpsChecker,
     AutocallChecker
 ]
 
 _default_handlers = [
     PrefilterHandler,
-    AliasHandler,
     MacroHandler,
     MagicHandler,
     AutoHandler,
diff --git a/IPython/core/tests/test_alias.py b/IPython/core/tests/test_alias.py
new file mode 100644
index 0000000..8ae57f6
--- /dev/null
+++ b/IPython/core/tests/test_alias.py
@@ -0,0 +1,41 @@
+from IPython.utils.capture import capture_output
+
+import nose.tools as nt
+
+def test_alias_lifecycle():
+    name = 'test_alias1'
+    cmd = 'echo "Hello"'
+    am = _ip.alias_manager
+    am.clear_aliases()
+    am.define_alias(name, cmd)
+    assert am.is_alias(name)
+    nt.assert_equal(am.retrieve_alias(name), cmd)
+    nt.assert_in((name, cmd), am.aliases)
+    
+    # Test running the alias
+    orig_system = _ip.system
+    result = []
+    _ip.system = result.append
+    try:
+        _ip.run_cell('%{}'.format(name))
+        result = [c.strip() for c in result]
+        nt.assert_equal(result, [cmd])
+    finally:
+        _ip.system = orig_system
+    
+    # Test removing the alias
+    am.undefine_alias(name)
+    assert not am.is_alias(name)
+    with nt.assert_raises(ValueError):
+        am.retrieve_alias(name)
+    nt.assert_not_in((name, cmd), am.aliases)
+    
+
+def test_alias_args_error():
+    """Error expanding with wrong number of arguments"""
+    _ip.alias_manager.define_alias('parts', 'echo first %s second %s')
+    # capture stderr:
+    with capture_output() as cap:
+        _ip.run_cell('parts 1')
+
+    nt.assert_equal(cap.stderr.split(':')[0], 'UsageError')
\ No newline at end of file
diff --git a/IPython/core/tests/test_handlers.py b/IPython/core/tests/test_handlers.py
index 5601717..20f956a 100644
--- a/IPython/core/tests/test_handlers.py
+++ b/IPython/core/tests/test_handlers.py
@@ -45,28 +45,6 @@ def run(tests):
 
 
 def test_handlers():
-    # alias expansion
-
-    # We're using 'true' as our syscall of choice because it doesn't
-    # write anything to stdout.
-
-    # Turn off actual execution of aliases, because it's noisy
-    old_system_cmd = ip.system
-    ip.system = lambda cmd: None
-
-
-    ip.alias_manager.alias_table['an_alias'] = (0, 'true')
-    # These are useful for checking a particular recursive alias issue
-    ip.alias_manager.alias_table['top'] = (0, 'd:/cygwin/top')
-    ip.alias_manager.alias_table['d'] =   (0, 'true')
-    run([(i,py3compat.u_format(o)) for i,o in \
-        [("an_alias",    "get_ipython().system({u}'true ')"),     # alias
-         # Below: recursive aliases should expand whitespace-surrounded
-         # chars, *not* initial chars which happen to be aliases:
-         ("top",         "get_ipython().system({u}'d:/cygwin/top ')"),
-         ]])
-    ip.system = old_system_cmd
-
     call_idx = CallableIndexable()
     ip.user_ns['call_idx'] = call_idx
 
diff --git a/IPython/core/tests/test_interactiveshell.py b/IPython/core/tests/test_interactiveshell.py
index 954f60c..ee6569c 100644
--- a/IPython/core/tests/test_interactiveshell.py
+++ b/IPython/core/tests/test_interactiveshell.py
@@ -106,17 +106,6 @@ class InteractiveShellTestCase(unittest.TestCase):
         ip.run_cell('a = """\n%exit\n"""')
         self.assertEqual(ip.user_ns['a'], '\n%exit\n')
     
-    def test_alias_crash(self):
-        """Errors in prefilter can't crash IPython"""
-        ip.run_cell('%alias parts echo first %s second %s')
-        # capture stderr:
-        save_err = io.stderr
-        io.stderr = StringIO()
-        ip.run_cell('parts 1')
-        err = io.stderr.getvalue()
-        io.stderr = save_err
-        self.assertEqual(err.split(':')[0], 'ERROR')
-    
     def test_trailing_newline(self):
         """test that running !(command) does not raise a SyntaxError"""
         ip.run_cell('!(true)\n', False)
diff --git a/IPython/core/tests/test_magic.py b/IPython/core/tests/test_magic.py
index fcf6c8c..d0953dd 100644
--- a/IPython/core/tests/test_magic.py
+++ b/IPython/core/tests/test_magic.py
@@ -48,16 +48,16 @@ class DummyMagics(magic.Magics): pass
 def test_rehashx():
     # clear up everything
     _ip = get_ipython()
-    _ip.alias_manager.alias_table.clear()
+    _ip.alias_manager.clear_aliases()
     del _ip.db['syscmdlist']
     
     _ip.magic('rehashx')
     # Practically ALL ipython development systems will have more than 10 aliases
 
-    nt.assert_true(len(_ip.alias_manager.alias_table) > 10)
-    for key, val in _ip.alias_manager.alias_table.iteritems():
+    nt.assert_true(len(_ip.alias_manager.aliases) > 10)
+    for name, cmd in _ip.alias_manager.aliases:
         # we must strip dots from alias names
-        nt.assert_not_in('.', key)
+        nt.assert_not_in('.', name)
 
     # rehashx must fill up syscmdlist
     scoms = _ip.db['syscmdlist']
diff --git a/IPython/extensions/storemagic.py b/IPython/extensions/storemagic.py
index b4c698f..aa7a7c1 100644
--- a/IPython/extensions/storemagic.py
+++ b/IPython/extensions/storemagic.py
@@ -210,17 +210,17 @@ class StoreMagics(Magics, Configurable):
                 obj = ip.user_ns[args[0]]
             except KeyError:
                 # it might be an alias
-                # This needs to be refactored to use the new AliasManager stuff.
-                if args[0] in ip.alias_manager:
-                    name = args[0]
-                    nargs, cmd = ip.alias_manager.alias_table[ name ]
-                    staliases = db.get('stored_aliases',{})
-                    staliases[ name ] = cmd
-                    db['stored_aliases'] = staliases
-                    print "Alias stored: %s (%s)" % (name, cmd)
-                    return
-                else:
-                    raise UsageError("Unknown variable '%s'" % args[0])
+                name = args[0]
+                try:
+                    cmd = ip.alias_manager.retrieve_alias(name)
+                except ValueError:
+                    raise UsageError("Unknown variable '%s'" % name)
+                
+                staliases = db.get('stored_aliases',{})
+                staliases[name] = cmd
+                db['stored_aliases'] = staliases
+                print "Alias stored: %s (%s)" % (name, cmd)
+                return
 
             else:
                 modname = getattr(inspect.getmodule(obj), '__name__', '')
diff --git a/IPython/extensions/tests/test_storemagic.py b/IPython/extensions/tests/test_storemagic.py
index 203ffd4..a5a15ba 100644
--- a/IPython/extensions/tests/test_storemagic.py
+++ b/IPython/extensions/tests/test_storemagic.py
@@ -27,7 +27,7 @@ def test_store_restore():
     # Check restoring
     ip.magic('store -r')
     nt.assert_equal(ip.user_ns['foo'], 78)
-    nt.assert_in('bar', ip.alias_manager.alias_table)
+    assert ip.alias_manager.is_alias('bar')
     nt.assert_in(os.path.realpath(tmpd), ip.user_ns['_dh'])
     
     os.rmdir(tmpd)
diff --git a/IPython/terminal/interactiveshell.py b/IPython/terminal/interactiveshell.py
index 3a7c93a..5b034d0 100644
--- a/IPython/terminal/interactiveshell.py
+++ b/IPython/terminal/interactiveshell.py
@@ -369,7 +369,7 @@ class TerminalInteractiveShell(InteractiveShell):
 
 
         for name, cmd in aliases:
-            self.alias_manager.define_alias(name, cmd)
+            self.alias_manager.soft_define_alias(name, cmd)
 
     #-------------------------------------------------------------------------
     # Things related to the banner and usage
diff --git a/docs/source/whatsnew/pr/incompat-drop-alias.rst b/docs/source/whatsnew/pr/incompat-drop-alias.rst
new file mode 100644
index 0000000..570a7cf
--- /dev/null
+++ b/docs/source/whatsnew/pr/incompat-drop-alias.rst
@@ -0,0 +1,3 @@
+- The alias system has been reimplemented to use magic functions. There should be little
+  visible difference while automagics are enabled, as they are by default, but parts of the
+  :class:`~IPython.core.alias.AliasManager` API have been removed.