diff --git a/flake8/engine.py b/flake8/engine.py
index 8676cb2..f21e804 100644
--- a/flake8/engine.py
+++ b/flake8/engine.py
@@ -10,6 +10,8 @@ from flake8.util import OrderedSet, is_windows, is_using_stdin
 
 _flake8_noqa = re.compile(r'flake8[:=]\s*noqa', re.I).search
 
+EXTRA_EXCLUDE = '.tox'
+
 
 def _register_extensions():
     """Register all the extensions."""
@@ -89,6 +91,9 @@ def get_style_guide(**kwargs):
     kwargs['parser'], options_hooks = get_parser()
     styleguide = StyleGuide(**kwargs)
     options = styleguide.options
+    # Add pattersn in EXTRA_EXCLUDE to the list of excluded patterns
+    options.exclude.extend(pep8.normalize_paths(EXTRA_EXCLUDE))
+
     for options_hook in options_hooks:
         options_hook(options)
 
diff --git a/flake8/main.py b/flake8/main.py
index d09535c..3b6d30c 100644
--- a/flake8/main.py
+++ b/flake8/main.py
@@ -15,7 +15,7 @@ else:
         'flake8'
     )
 
-EXTRA_IGNORE = ['.tox']
+EXTRA_IGNORE = []
 
 
 def main():