diff --git a/flake8/run.py b/flake8/run.py
index 3ca0249..f0f5012 100644
--- a/flake8/run.py
+++ b/flake8/run.py
@@ -44,11 +44,11 @@ def _get_python_files(paths):
                     if not filename.endswith('.py'):
                         continue
                     fullpath = os.path.join(dirpath, filename)
-                    if not skip_file(fullpath):
+                    if not skip_file(fullpath, pep8style):
                         yield fullpath
 
         else:
-            if not skip_file(path):
+            if not skip_file(path, pep8style):
                 yield path
 
 
@@ -92,7 +92,7 @@ def _get_files(repo, **kwargs):
             seen.add(file_)
             if not file_.endswith('.py'):
                 continue
-            if skip_file(file_):
+            if skip_file(file_, pep8style):
                 continue
             yield file_
 
diff --git a/flake8/util.py b/flake8/util.py
index bb3f4b6..9ab86ef 100644
--- a/flake8/util.py
+++ b/flake8/util.py
@@ -22,7 +22,7 @@ def skip_line(line):
 _NOQA = re.compile(r'flake8[:=]\s*noqa', re.I | re.M)
 
 
-def skip_file(path):
+def skip_file(path, pep8style):
     """Returns True if this header is found in path
 
     # flake8: noqa
@@ -32,4 +32,4 @@ def skip_file(path):
         content = f.read()
     finally:
         f.close()
-    return _NOQA.search(content) is not None
+    return _NOQA.search(content) is not None or pep8style.excluded(path)