diff --git a/docs/source/user/options.rst b/docs/source/user/options.rst
index 1cbc22f..00164ae 100644
--- a/docs/source/user/options.rst
+++ b/docs/source/user/options.rst
@@ -58,6 +58,8 @@ Index of Options
 
 - :option:`flake8 --extend-ignore`
 
+- :option:`flake8 --per-file-ignores`
+
 - :option:`flake8 --max-line-length`
 
 - :option:`flake8 --select`
@@ -422,6 +424,8 @@ Options and their Descriptions
 
     :ref:`Go back to index <top>`
 
+    .. versionadded:: 3.6.0
+
     Specify a list of codes to add to the list of ignored ones. Similar
     considerations as in :option:`--ignore` apply here with regard to the
     value.
@@ -449,6 +453,40 @@ Options and their Descriptions
         extend-ignore = E4,E51,W234
 
 
+.. option:: --per-file-ignores=<filename:errors>[ <filename:errors>]
+
+    :ref:`Go back to index <top>`
+
+    .. versionadded:: 3.7.0
+
+    Specify a list of mappings of files and the codes that should be ignored
+    for the entirety of the file. This allows for a project to have a default
+    list of violations that should be ignored as well as file-specific
+    violations for files that have not been made compliant with the project
+    rules.
+
+    This option supports syntax similar to :option:`--exclude` such that glob
+    patterns will also work here.
+
+    This can be combined with both :option:`--ignore` and
+    :option:`--extend-ignore` to achieve a full flexibility of style options.
+
+    Command-line usage:
+
+    .. prompt:: bash
+
+        flake8 --per-file-ignores='project/__init__.py:F401 setup.py:E121'
+        flake8 --per-file-ignores='project/*/__init__.py:F401 setup.py:E121'
+
+    This **can** be specified in config files.
+
+    .. code-block:: ini
+
+        per-file-ignores =
+            project/__init__.py:F401
+            setup.py:E121
+            other_project/*:W9
+
 .. option:: --max-line-length=<n>
 
     :ref:`Go back to index <top>`
@@ -743,6 +781,8 @@ Options and their Descriptions
 
     :ref:`Go back to index <top>`
 
+    .. versionadded:: 3.6.0
+
     Provide extra config files to parse in after and in addition to the files
     that |Flake8| found on its own. Since these files are the last ones read
     into the Configuration Parser, so it has the highest precedence if it
diff --git a/src/flake8/__init__.py b/src/flake8/__init__.py
index 5f316c9..c15bf87 100644
--- a/src/flake8/__init__.py
+++ b/src/flake8/__init__.py
@@ -15,7 +15,7 @@ import sys
 LOG = logging.getLogger(__name__)
 LOG.addHandler(logging.NullHandler())
 
-__version__ = "3.6.0"
+__version__ = "3.7.0dev0"
 __version_info__ = tuple(
     int(i) for i in __version__.split(".") if i.isdigit()
 )
diff --git a/src/flake8/checker.py b/src/flake8/checker.py
index e8a71d4..3b97414 100644
--- a/src/flake8/checker.py
+++ b/src/flake8/checker.py
@@ -2,7 +2,6 @@
 import collections
 import errno
 import logging
-import os
 import signal
 import sys
 import tokenize
@@ -188,20 +187,12 @@ class Manager(object):
                 return False
             path = self.options.stdin_display_name
 
-        exclude = self.options.exclude
-        if not exclude:
-            return False
-        basename = os.path.basename(path)
-        if utils.fnmatch(basename, exclude):
-            LOG.debug('"%s" has been excluded', basename)
-            return True
-
-        absolute_path = os.path.abspath(path)
-        match = utils.fnmatch(absolute_path, exclude)
-        LOG.debug(
-            '"%s" has %sbeen excluded', absolute_path, "" if match else "not "
+        return utils.matches_filename(
+            path,
+            patterns=self.options.exclude,
+            log_message='"%(path)s" has %(whether)sbeen excluded',
+            logger=LOG,
         )
-        return match
 
     def make_checkers(self, paths=None):
         # type: (List[str]) -> NoneType
diff --git a/src/flake8/main/application.py b/src/flake8/main/application.py
index bd409d7..b86b3cc 100644
--- a/src/flake8/main/application.py
+++ b/src/flake8/main/application.py
@@ -65,8 +65,8 @@ class Application(object):
         self.formatter = None
         #: The :class:`flake8.plugins.notifier.Notifier` for listening plugins
         self.listener_trie = None
-        #: The :class:`flake8.style_guide.StyleGuide` built from the user's
-        #: options
+        #: The :class:`flake8.style_guide.StyleGuideManager` built from the
+        #: user's options
         self.guide = None
         #: The :class:`flake8.checker.Manager` that will handle running all of
         #: the checks selected by the user.
@@ -283,7 +283,7 @@ class Application(object):
         # type: () -> NoneType
         """Initialize our StyleGuide."""
         if self.guide is None:
-            self.guide = style_guide.StyleGuide(
+            self.guide = style_guide.StyleGuideManager(
                 self.options, self.listener_trie, self.formatter
             )
 
diff --git a/src/flake8/main/options.py b/src/flake8/main/options.py
index 73b3932..2aabab8 100644
--- a/src/flake8/main/options.py
+++ b/src/flake8/main/options.py
@@ -1,5 +1,6 @@
 """Contains the logic for all of the default options for Flake8."""
 from flake8 import defaults
+from flake8 import utils
 from flake8.main import debug
 from flake8.main import vcs
 
@@ -19,6 +20,7 @@ def register_default_options(option_manager):
     - ``--hang-closing``
     - ``--ignore``
     - ``--extend-ignore``
+    - ``--per-file-ignores``
     - ``--max-line-length``
     - ``--select``
     - ``--disable-noqa``
@@ -142,6 +144,18 @@ def register_default_options(option_manager):
         " of ignored ones. For example, ``--extend-ignore=E4,E51,W234``.",
     )
 
+    add_option(
+        "--per-file-ignores",
+        parse_from_config=True,
+        comma_separated_list=True,
+        separator=utils.NEWLINE_SEPARATED_LIST_RE,
+        help="A pairing of filenames and violation codes that defines which "
+        "violations to ignore in a particular file. The filenames can be "
+        "specified in a manner similar to the ``--exclude`` option and the "
+        "violations work similarly to the ``--ignore`` and ``--select`` "
+        "options.",
+    )
+
     add_option(
         "--max-line-length",
         type="int",
diff --git a/src/flake8/options/manager.py b/src/flake8/options/manager.py
index 3f4e883..7be4315 100644
--- a/src/flake8/options/manager.py
+++ b/src/flake8/options/manager.py
@@ -32,6 +32,7 @@ class Option(object):
         parse_from_config=False,
         comma_separated_list=False,
         normalize_paths=False,
+        separator=None,
     ):
         """Initialize an Option instance wrapping optparse.Option.
 
@@ -79,6 +80,8 @@ class Option(object):
         :param bool normalize_paths:
             Whether the option is expecting a path or list of paths and should
             attempt to normalize the paths to absolute paths.
+        :param separator:
+            The item that separates the "comma"-separated list.
         """
         self.short_option_name = short_option_name
         self.long_option_name = long_option_name
@@ -107,6 +110,7 @@ class Option(object):
         self.parse_from_config = parse_from_config
         self.comma_separated_list = comma_separated_list
         self.normalize_paths = normalize_paths
+        self.separator = separator or utils.COMMA_SEPARATED_LIST_RE
 
         self.config_name = None
         if parse_from_config:
diff --git a/src/flake8/style_guide.py b/src/flake8/style_guide.py
index 7565b00..46f72fc 100644
--- a/src/flake8/style_guide.py
+++ b/src/flake8/style_guide.py
@@ -1,6 +1,7 @@
 """Implementation of the StyleGuide used by Flake8."""
 import collections
 import contextlib
+import copy
 import enum
 import functools
 import itertools
@@ -321,8 +322,8 @@ class DecisionEngine(object):
         return decision
 
 
-class StyleGuide(object):
-    """Manage a Flake8 user's style guide."""
+class StyleGuideManager(object):
+    """Manage multiple style guides for a single run."""
 
     def __init__(self, options, listener_trie, formatter, decider=None):
         """Initialize our StyleGuide.
@@ -334,8 +335,136 @@ class StyleGuide(object):
         self.formatter = formatter
         self.stats = statistics.Statistics()
         self.decider = decider or DecisionEngine(options)
+        self.style_guides = []
+        self.default_style_guide = StyleGuide(
+            options, listener_trie, formatter, decider=decider
+        )
+        self.style_guides = list(
+            itertools.chain(
+                [self.default_style_guide],
+                self.populate_style_guides_with(options),
+            )
+        )
+
+    def populate_style_guides_with(self, options):
+        """Generate style guides from the per-file-ignores option.
+
+        :param options:
+            The original options parsed from the CLI and config file.
+        :type options:
+            :class:`~optparse.Values`
+        :returns:
+            A copy of the default style guide with overridden values.
+        :rtype:
+            :class:`~flake8.style_guide.StyleGuide`
+        """
+        for value in options.per_file_ignores:
+            filename, violations_str = value.split(":")
+            violations = utils.parse_comma_separated_list(violations_str)
+            yield self.default_style_guide.copy(
+                filename=filename, extend_ignore_with=violations
+            )
+
+    def style_guide_for(self, filename):
+        """Find the StyleGuide for the filename in particular."""
+        guides = sorted(
+            (g for g in self.style_guides if g.applies_to(filename)),
+            key=lambda g: len(g.filename or ""),
+        )
+        if len(guides) > 1:
+            return guides[-1]
+        return guides[0]
+
+    @contextlib.contextmanager
+    def processing_file(self, filename):
+        """Record the fact that we're processing the file's results."""
+        guide = self.style_guide_for(filename)
+        with guide.processing_file(filename):
+            yield guide
+
+    def handle_error(
+        self,
+        code,
+        filename,
+        line_number,
+        column_number,
+        text,
+        physical_line=None,
+    ):
+        # type: (str, str, int, int, str) -> int
+        """Handle an error reported by a check.
+
+        :param str code:
+            The error code found, e.g., E123.
+        :param str filename:
+            The file in which the error was found.
+        :param int line_number:
+            The line number (where counting starts at 1) at which the error
+            occurs.
+        :param int column_number:
+            The column number (where counting starts at 1) at which the error
+            occurs.
+        :param str text:
+            The text of the error message.
+        :param str physical_line:
+            The actual physical line causing the error.
+        :returns:
+            1 if the error was reported. 0 if it was ignored. This is to allow
+            for counting of the number of errors found that were not ignored.
+        :rtype:
+            int
+        """
+        guide = self.style_guide_for(filename)
+        return guide.handle_error(
+            code, filename, line_number, column_number, text, physical_line
+        )
+
+    def add_diff_ranges(self, diffinfo):
+        """Update the StyleGuides to filter out information not in the diff.
+
+        This provides information to the underlying StyleGuides so that only
+        the errors in the line number ranges are reported.
+
+        :param dict diffinfo:
+            Dictionary mapping filenames to sets of line number ranges.
+        """
+        for guide in self.style_guides.values():
+            guide.add_diff_ranges(diffinfo)
+
+
+class StyleGuide(object):
+    """Manage a Flake8 user's style guide."""
+
+    def __init__(
+        self, options, listener_trie, formatter, filename=None, decider=None
+    ):
+        """Initialize our StyleGuide.
+
+        .. todo:: Add parameter documentation.
+        """
+        self.options = options
+        self.listener = listener_trie
+        self.formatter = formatter
+        self.stats = statistics.Statistics()
+        self.decider = decider or DecisionEngine(options)
+        self.filename = filename
+        if self.filename:
+            self.filename = utils.normalize_path(self.filename)
         self._parsed_diff = {}
 
+    def __repr__(self):
+        """Make it easier to debug which StyleGuide we're using."""
+        return "<StyleGuide [{}]>".format(self.filename)
+
+    def copy(self, filename=None, extend_ignore_with=None, **kwargs):
+        """Create a copy of this style guide with different values."""
+        filename = filename or self.filename
+        options = copy.deepcopy(self.options)
+        options.ignore.extend(extend_ignore_with or [])
+        return StyleGuide(
+            options, self.listener, self.formatter, filename=filename
+        )
+
     @contextlib.contextmanager
     def processing_file(self, filename):
         """Record the fact that we're processing the file's results."""
@@ -343,6 +472,26 @@ class StyleGuide(object):
         yield self
         self.formatter.finished(filename)
 
+    def applies_to(self, filename):
+        """Check if this StyleGuide applies to the file.
+
+        :param str filename:
+            The name of the file with violations that we're potentially
+            applying this StyleGuide to.
+        :returns:
+            True if this applies, False otherwise
+        :rtype:
+            bool
+        """
+        if self.filename is None:
+            return True
+        return utils.matches_filename(
+            filename,
+            patterns=[self.filename],
+            log_message='{!r} does %(whether)smatch "%(path)s"'.format(self),
+            logger=LOG,
+        )
+
     def should_report_error(self, code):
         # type: (str) -> Decision
         """Determine if the error code should be reported or ignored.
diff --git a/src/flake8/utils.py b/src/flake8/utils.py
index a837577..68627af 100644
--- a/src/flake8/utils.py
+++ b/src/flake8/utils.py
@@ -11,6 +11,7 @@ import tokenize
 
 DIFF_HUNK_REGEXP = re.compile(r"^@@ -\d+(?:,\d+)? \+(\d+)(?:,(\d+))? @@.*$")
 COMMA_SEPARATED_LIST_RE = re.compile(r"[,\s]")
+NEWLINE_SEPARATED_LIST_RE = re.compile(r"[\s]")
 LOCAL_PLUGIN_LIST_RE = re.compile(r"[,\t\n\r\f\v]")
 
 
@@ -335,6 +336,38 @@ def parameters_for(plugin):
     return parameters
 
 
+def matches_filename(path, patterns, log_message, logger):
+    """Use fnmatch to discern if a path exists in patterns.
+
+    :param str path:
+        The path to the file under question
+    :param patterns:
+        The patterns to match the path against.
+    :type patterns:
+        list[str]
+    :param str log_message:
+        The message used for logging purposes.
+    :returns:
+        True if path matches patterns, False otherwise
+    :rtype:
+        bool
+    """
+    if not patterns:
+        return False
+    basename = os.path.basename(path)
+    if fnmatch(basename, patterns):
+        logger.debug(log_message, {"path": basename, "whether": ""})
+        return True
+
+    absolute_path = os.path.abspath(path)
+    match = fnmatch(absolute_path, patterns)
+    logger.debug(
+        log_message,
+        {"path": absolute_path, "whether": "" if match else "not "},
+    )
+    return match
+
+
 def get_python_version():
     """Find and format the python implementation and version.
 
diff --git a/tests/unit/test_style_guide.py b/tests/unit/test_style_guide.py
index c9005ab..c4ef5ef 100644
--- a/tests/unit/test_style_guide.py
+++ b/tests/unit/test_style_guide.py
@@ -5,6 +5,7 @@ import mock
 import pytest
 
 from flake8 import style_guide
+from flake8 import utils
 from flake8.formatting import base
 from flake8.plugins import notifier
 
@@ -17,6 +18,7 @@ def create_options(**kwargs):
     kwargs.setdefault('extend_ignore', [])
     kwargs.setdefault('disable_noqa', False)
     kwargs.setdefault('enable_extensions', [])
+    kwargs.setdefault('per_file_ignores', [])
     return optparse.Values(kwargs)
 
 
@@ -81,3 +83,101 @@ def test_handle_error_does_not_notify_listeners(select_list, ignore_list,
         guide.handle_error(error_code, 'stdin', 1, 1, 'error found')
     assert listener_trie.notify.called is False
     assert formatter.handle.called is False
+
+
+def test_style_guide_manager():
+    """Verify how the StyleGuideManager creates a default style guide."""
+    listener_trie = mock.create_autospec(notifier.Notifier, instance=True)
+    formatter = mock.create_autospec(base.BaseFormatter, instance=True)
+    options = create_options()
+    guide = style_guide.StyleGuideManager(options,
+                                          listener_trie=listener_trie,
+                                          formatter=formatter)
+    assert guide.default_style_guide.options is options
+    assert len(guide.style_guides) == 1
+
+
+PER_FILE_IGNORES_UNPARSED = [
+    "first_file.py:W9",
+    "second_file.py:F4,F9",
+    "third_file.py:E3",
+    "sub_dir/*:F4",
+]
+
+
+@pytest.mark.parametrize('style_guide_file,filename,expected', [
+    ("first_file.py", "first_file.py", True),
+    ("first_file.py", "second_file.py", False),
+    ("sub_dir/*.py", "first_file.py", False),
+    ("sub_dir/*.py", "sub_dir/file.py", True),
+    ("sub_dir/*.py", "other_dir/file.py", False),
+])
+def test_style_guide_applies_to(style_guide_file, filename, expected):
+    """Verify that we match a file to its style guide."""
+    listener_trie = mock.create_autospec(notifier.Notifier, instance=True)
+    formatter = mock.create_autospec(base.BaseFormatter, instance=True)
+    options = create_options()
+    guide = style_guide.StyleGuide(options,
+                                   listener_trie=listener_trie,
+                                   formatter=formatter,
+                                   filename=style_guide_file)
+    assert guide.applies_to(filename) is expected
+
+
+def test_style_guide_manager_pre_file_ignores_parsing():
+    """Verify how the StyleGuideManager creates a default style guide."""
+    listener_trie = mock.create_autospec(notifier.Notifier, instance=True)
+    formatter = mock.create_autospec(base.BaseFormatter, instance=True)
+    options = create_options(per_file_ignores=PER_FILE_IGNORES_UNPARSED)
+    guide = style_guide.StyleGuideManager(options,
+                                          listener_trie=listener_trie,
+                                          formatter=formatter)
+    assert len(guide.style_guides) == 5
+    assert list(map(utils.normalize_path,
+                    ["first_file.py", "second_file.py", "third_file.py",
+                        "sub_dir/*"])
+                ) == [g.filename for g in guide.style_guides[1:]]
+
+
+@pytest.mark.parametrize('ignores,violation,filename,handle_error_return', [
+    (['E1', 'E2'], 'F401', 'first_file.py', 1),
+    (['E1', 'E2'], 'E121', 'first_file.py', 0),
+    (['E1', 'E2'], 'F401', 'second_file.py', 0),
+    (['E1', 'E2'], 'F401', 'third_file.py', 1),
+    (['E1', 'E2'], 'E311', 'third_file.py', 0),
+    (['E1', 'E2'], 'F401', 'sub_dir/file.py', 0),
+])
+def test_style_guide_manager_pre_file_ignores(ignores, violation, filename,
+                                              handle_error_return):
+    """Verify how the StyleGuideManager creates a default style guide."""
+    listener_trie = mock.create_autospec(notifier.Notifier, instance=True)
+    formatter = mock.create_autospec(base.BaseFormatter, instance=True)
+    options = create_options(ignore=ignores,
+                             select=['E', 'F', 'W'],
+                             per_file_ignores=PER_FILE_IGNORES_UNPARSED)
+    guide = style_guide.StyleGuideManager(options,
+                                          listener_trie=listener_trie,
+                                          formatter=formatter)
+    assert (guide.handle_error(violation, filename, 1, 1, "Fake text")
+            == handle_error_return)
+
+
+@pytest.mark.parametrize('filename,expected', [
+    ('first_file.py', utils.normalize_path('first_file.py')),
+    ('second_file.py', utils.normalize_path('second_file.py')),
+    ('third_file.py', utils.normalize_path('third_file.py')),
+    ('fourth_file.py', None),
+    ('sub_dir/__init__.py', utils.normalize_path('sub_dir/*')),
+    ('other_dir/__init__.py', None),
+])
+def test_style_guide_manager_style_guide_for(filename, expected):
+    """Verify the style guide selection function."""
+    listener_trie = mock.create_autospec(notifier.Notifier, instance=True)
+    formatter = mock.create_autospec(base.BaseFormatter, instance=True)
+    options = create_options(per_file_ignores=PER_FILE_IGNORES_UNPARSED)
+    guide = style_guide.StyleGuideManager(options,
+                                          listener_trie=listener_trie,
+                                          formatter=formatter)
+
+    file_guide = guide.style_guide_for(filename)
+    assert file_guide.filename == expected