Steps to reproduce Call pylint from a python script as: (pylint_stdout, pylint_stderr) = lint.py_run(command_options = "%s -E --msg-template={path} {msg} my_module.py", return_std=True) and print the output of pylint_stdout.readlines() Current behavior When printed, pylint_stdout is not formatted as defined in command_options (see above), but instead, the message is shown as defined in pylint/eplyint.py (line 90-92): cmd = [sys.executable, "-c", run_cmd] + options + [ '--msg-template', '{path}:{line}: {category} ({msg_id}, {symbol}, {obj}) {msg}', '-r', 'n', child_path] Expected behavior The output when printing pylint_stdout.readlines() should be: PATH MSG But you get, instead: PATH:188: error (E1101, no-member, OBJECT) MESSAGE pylint --version output No config file found, using default configuration pylint 1.6.4, astroid 1.4.8 Python 2.7.6 (default, Oct 26 2016, 20:30:19) [GCC 4.8.4] From: https://github.com/PyCQA/pylint/issues/1269