diff --git a/CHANGES b/CHANGES
index 157e92e3..62bb2004 100644
--- a/CHANGES
+++ b/CHANGES
@@ -8,6 +8,10 @@ Version 0.13
 
 Major release, unreleased
 
+- Make `app.run()` into a noop if a Flask application is run from the
+  development server on the command line.  This avoids some behavior that
+  was confusing to debug for newcomers.
+
 Version 0.12.1
 --------------
 
diff --git a/flask/app.py b/flask/app.py
index 92ee8772..27918d01 100644
--- a/flask/app.py
+++ b/flask/app.py
@@ -824,6 +824,13 @@ class Flask(_PackageBoundObject):
                         :func:`werkzeug.serving.run_simple` for more
                         information.
         """
+        # Change this into a no-op if the server is invoked from the
+        # command line.  Have a look at cli.py for more information.
+        if os.environ.get('FLASK_RUN_FROM_CLI_SERVER') == '1':
+            from .debughelpers import explain_ignored_app_run
+            explain_ignored_app_run()
+            return
+
         from werkzeug.serving import run_simple
         _host = '127.0.0.1'
         _port = 5000
diff --git a/flask/cli.py b/flask/cli.py
index 074ee768..bde5a13b 100644
--- a/flask/cli.py
+++ b/flask/cli.py
@@ -412,6 +412,13 @@ def run_command(info, host, port, reload, debugger, eager_loading,
     """
     from werkzeug.serving import run_simple
 
+    # Set a global flag that indicates that we were invoked from the
+    # command line interface provided server command.  This is detected
+    # by Flask.run to make the call into a no-op.  This is necessary to
+    # avoid ugly errors when the script that is loaded here also attempts
+    # to start a server.
+    os.environ['FLASK_RUN_FROM_CLI_SERVER'] = '1'
+
     debug = get_debug_flag()
     if reload is None:
         reload = bool(debug)
diff --git a/flask/debughelpers.py b/flask/debughelpers.py
index 90710dd3..9e44fe69 100644
--- a/flask/debughelpers.py
+++ b/flask/debughelpers.py
@@ -8,6 +8,9 @@
     :copyright: (c) 2015 by Armin Ronacher.
     :license: BSD, see LICENSE for more details.
 """
+import os
+from warnings import warn
+
 from ._compat import implements_to_string, text_type
 from .app import Flask
 from .blueprints import Blueprint
@@ -153,3 +156,12 @@ def explain_template_loading_attempts(app, template, attempts):
         info.append('  See http://flask.pocoo.org/docs/blueprints/#templates')
 
     app.logger.info('\n'.join(info))
+
+
+def explain_ignored_app_run():
+    if os.environ.get('WERKZEUG_RUN_MAIN') != 'true':
+        warn(Warning('Silently ignoring app.run() because the '
+                     'application is run from the flask command line '
+                     'executable.  Consider putting app.run() behind an '
+                     'if __name__ == "__main__" guard to silence this '
+                     'warning.'), stacklevel=3)