diff --git a/IPython/core/alias.py b/IPython/core/alias.py
index e1a6242..aa55137 100644
--- a/IPython/core/alias.py
+++ b/IPython/core/alias.py
@@ -151,8 +151,8 @@ class Alias(object):
             raise InvalidAliasError("An alias command must be a string, "
                                     "got: %r" % self.cmd)
 
-        nargs = self.cmd.count('%s')
-
+        nargs = self.cmd.count('%s') - 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.')
@@ -169,7 +169,10 @@ class Alias(object):
         if cmd.find('%l') >= 0:
             cmd = cmd.replace('%l', rest)
             rest = ''
+        
         if nargs==0:
+            if cmd.find('%%s') >= 1:
+                cmd = cmd.replace('%%s', '%s')
             # Simple, argument-less aliases
             cmd = '%s %s' % (cmd, rest)
         else:
diff --git a/IPython/core/tests/test_alias.py b/IPython/core/tests/test_alias.py
index 8ae57f6..7417e95 100644
--- a/IPython/core/tests/test_alias.py
+++ b/IPython/core/tests/test_alias.py
@@ -38,4 +38,25 @@ def test_alias_args_error():
     with capture_output() as cap:
         _ip.run_cell('parts 1')
 
-    nt.assert_equal(cap.stderr.split(':')[0], 'UsageError')
\ No newline at end of file
+    nt.assert_equal(cap.stderr.split(':')[0], 'UsageError')
+    
+def test_alias_args_commented():
+    """Check that alias correctly ignores 'commented out' args"""
+    _ip.magic('alias commetarg echo this is %%s a commented out arg')
+    
+    with capture_output() as cap:
+        _ip.run_cell('commetarg')
+    
+    nt.assert_equal(cap.stdout, 'this is %s a commented out arg')
+
+def test_alias_args_commented_nargs():
+    """Check that alias correctly counts args, excluding those commented out"""
+    am = _ip.alias_manager
+    alias_name = 'comargcount'
+    cmd = 'echo this is %%s a commented out arg and this is not %s'
+    
+    am.define_alias(alias_name, cmd)
+    assert am.is_alias(alias_name)
+    
+    thealias = am.get_alias(alias_name)
+    nt.assert_equal(thealias.nargs, 1)
\ No newline at end of file