diff --git a/IPython/core/magics/execution.py b/IPython/core/magics/execution.py
index ef9ae1b..0d036e1 100644
--- a/IPython/core/magics/execution.py
+++ b/IPython/core/magics/execution.py
@@ -849,6 +849,7 @@ python-profiler package from non-free.""")
         bdb.Breakpoint.next = 1
         bdb.Breakpoint.bplist = {}
         bdb.Breakpoint.bpbynumber = [None]
+        deb.clear_all_breaks()
         if bp_line is not None:
             # Set an initial breakpoint to stop execution
             maxtries = 10
diff --git a/IPython/core/tests/test_run.py b/IPython/core/tests/test_run.py
index e089413..1b904f0 100644
--- a/IPython/core/tests/test_run.py
+++ b/IPython/core/tests/test_run.py
@@ -165,8 +165,8 @@ def doctest_reset_del():
 class TestMagicRunPass(tt.TempFileMixin):
 
     def setup(self):
-        """Make a valid python temp file."""
-        self.mktmp('pass\n')
+        content = "a = [1,2,3]\nb = 1"
+        self.mktmp(content)
         
     def run_tmpfile(self):
         _ip = get_ipython()
@@ -213,6 +213,16 @@ class TestMagicRunPass(tt.TempFileMixin):
         with tt.fake_input(['c']):
             _ip.magic('run -d %s' % self.fname)
 
+    def test_run_debug_twice_with_breakpoint(self):
+        """Make a valid python temp file."""
+        _ip = get_ipython()
+        with tt.fake_input(['b 2', 'c', 'c']):
+            _ip.magic('run -d %s' % self.fname)
+
+        with tt.fake_input(['c']):
+            with tt.AssertNotPrints('KeyError'):
+                _ip.magic('run -d %s' % self.fname)
+
 
 class TestMagicRunSimple(tt.TempFileMixin):