diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 47a77a3e3..9f108f189 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -225,6 +225,11 @@ time or change existing behaviors in order to make them less surprising/more use
 * ``yield``-based tests are considered deprecated and will be removed in pytest-4.0.
   Thanks `@nicoddemus`_ for the PR.
 
+* ``[pytest]`` sections in ``setup.cfg`` files should now be named ``[tool:pytest]``
+  to avoid conflicts with other distutils commands (see `#567`_). ``[pytest]`` sections in
+  ``pytest.ini`` or ``tox.ini`` files are supported and unchanged.
+  Thanks `@nicoddemus`_ for the PR.
+
 * Using ``pytest_funcarg__`` prefix to declare fixtures is considered deprecated and will be
   removed in pytest-4.0 (`#1684`_).
   Thanks `@nicoddemus`_ for the PR.
@@ -375,6 +380,7 @@ time or change existing behaviors in order to make them less surprising/more use
 .. _#372: https://github.com/pytest-dev/pytest/issues/372
 .. _#457: https://github.com/pytest-dev/pytest/issues/457
 .. _#460: https://github.com/pytest-dev/pytest/pull/460
+.. _#567: https://github.com/pytest-dev/pytest/pull/567
 .. _#607: https://github.com/pytest-dev/pytest/issues/607
 .. _#634: https://github.com/pytest-dev/pytest/issues/634
 .. _#717: https://github.com/pytest-dev/pytest/issues/717
diff --git a/_pytest/config.py b/_pytest/config.py
index 4756df1d1..2a1215811 100644
--- a/_pytest/config.py
+++ b/_pytest/config.py
@@ -927,7 +927,7 @@ class Config(object):
 
     def _initini(self, args):
         ns, unknown_args = self._parser.parse_known_and_unknown_args(args, namespace=self.option.copy())
-        r = determine_setup(ns.inifilename, ns.file_or_dir + unknown_args)
+        r = determine_setup(ns.inifilename, ns.file_or_dir + unknown_args, warnfunc=self.warn)
         self.rootdir, self.inifile, self.inicfg = r
         self._parser.extra_info['rootdir'] = self.rootdir
         self._parser.extra_info['inifile'] = self.inifile
@@ -1154,7 +1154,18 @@ def exists(path, ignore=EnvironmentError):
     except ignore:
         return False
 
-def getcfg(args, inibasenames):
+def getcfg(args, warnfunc=None):
+    """
+    Search the list of arguments for a valid ini-file for pytest,
+    and return a tuple of (rootdir, inifile, cfg-dict).
+
+    note: warnfunc is an optional function used to warn
+        about ini-files that use deprecated features.
+        This parameter should be removed when pytest
+        adopts standard deprecation warnings (#1804).
+    """
+    from _pytest.deprecated import SETUP_CFG_PYTEST
+    inibasenames = ["pytest.ini", "tox.ini", "setup.cfg"]
     args = [x for x in args if not str(x).startswith("-")]
     if not args:
         args = [py.path.local()]
@@ -1166,7 +1177,11 @@ def getcfg(args, inibasenames):
                 if exists(p):
                     iniconfig = py.iniconfig.IniConfig(p)
                     if 'pytest' in iniconfig.sections:
+                        if inibasename == 'setup.cfg' and warnfunc:
+                            warnfunc('C1', SETUP_CFG_PYTEST)
                         return base, p, iniconfig['pytest']
+                    if inibasename == 'setup.cfg' and 'tool:pytest' in iniconfig.sections:
+                        return base, p, iniconfig['tool:pytest']
                     elif inibasename == "pytest.ini":
                         # allowed to be empty
                         return base, p, {}
@@ -1207,7 +1222,7 @@ def get_dirs_from_args(args):
             if d.exists()]
 
 
-def determine_setup(inifile, args):
+def determine_setup(inifile, args, warnfunc=None):
     dirs = get_dirs_from_args(args)
     if inifile:
         iniconfig = py.iniconfig.IniConfig(inifile)
@@ -1218,15 +1233,13 @@ def determine_setup(inifile, args):
         rootdir = get_common_ancestor(dirs)
     else:
         ancestor = get_common_ancestor(dirs)
-        rootdir, inifile, inicfg = getcfg(
-            [ancestor], ["pytest.ini", "tox.ini", "setup.cfg"])
+        rootdir, inifile, inicfg = getcfg([ancestor], warnfunc=warnfunc)
         if rootdir is None:
             for rootdir in ancestor.parts(reverse=True):
                 if rootdir.join("setup.py").exists():
                     break
             else:
-                rootdir, inifile, inicfg = getcfg(
-                    dirs, ["pytest.ini", "tox.ini", "setup.cfg"])
+                rootdir, inifile, inicfg = getcfg(dirs, warnfunc=warnfunc)
                 if rootdir is None:
                     rootdir = get_common_ancestor([py.path.local(), ancestor])
                     is_fs_root = os.path.splitdrive(str(rootdir))[1] == os.sep
diff --git a/_pytest/deprecated.py b/_pytest/deprecated.py
index 7d8c747af..6edc475f6 100644
--- a/_pytest/deprecated.py
+++ b/_pytest/deprecated.py
@@ -17,6 +17,8 @@ FUNCARG_PREFIX = (
     'and scheduled to be removed in pytest 4.0.  '
     'Please remove the prefix and use the @pytest.fixture decorator instead.')
 
+SETUP_CFG_PYTEST = '[pytest] section in setup.cfg files is deprecated, use [tool:pytest] instead.'
+
 GETFUNCARGVALUE = "use of getfuncargvalue is deprecated, use getfixturevalue"
 
 RESULT_LOG = '--result-log is deprecated and scheduled for removal in pytest 4.0'
diff --git a/_pytest/helpconfig.py b/_pytest/helpconfig.py
index f92ce1c04..84f419a08 100644
--- a/_pytest/helpconfig.py
+++ b/_pytest/helpconfig.py
@@ -71,7 +71,6 @@ def showhelp(config):
     tw.write(config._parser.optparser.format_help())
     tw.line()
     tw.line()
-    #tw.sep( "=", "config file settings")
     tw.line("[pytest] ini-options in the next "
             "pytest.ini|tox.ini|setup.cfg file:")
     tw.line()
diff --git a/doc/en/customize.rst b/doc/en/customize.rst
index 54cf43249..7ca8d1215 100644
--- a/doc/en/customize.rst
+++ b/doc/en/customize.rst
@@ -50,7 +50,7 @@ Here is the algorithm which finds the rootdir from ``args``:
 
 Note that an existing ``pytest.ini`` file will always be considered a match,
 whereas ``tox.ini`` and ``setup.cfg`` will only match if they contain a
-``[pytest]`` section. Options from multiple ini-files candidates are never
+``[pytest]`` or ``[tool:pytest]`` section, respectively. Options from multiple ini-files candidates are never
 merged - the first one wins (``pytest.ini`` always wins, even if it does not
 contain a ``[pytest]`` section).
 
@@ -73,7 +73,7 @@ check for ini-files as follows::
 
     # first look for pytest.ini files
     path/pytest.ini
-    path/setup.cfg  # must also contain [pytest] section to match
+    path/setup.cfg  # must also contain [tool:pytest] section to match
     path/tox.ini    # must also contain [pytest] section to match
     pytest.ini
     ... # all the way down to the root
@@ -154,7 +154,7 @@ Builtin configuration file options
 
    .. code-block:: ini
 
-        # content of setup.cfg
+        # content of pytest.ini
         [pytest]
         norecursedirs = .svn _build tmp*
 
diff --git a/doc/en/example/pythoncollection.rst b/doc/en/example/pythoncollection.rst
index 0e481271a..c565506c4 100644
--- a/doc/en/example/pythoncollection.rst
+++ b/doc/en/example/pythoncollection.rst
@@ -77,9 +77,9 @@ Example::
 Changing directory recursion
 -----------------------------------------------------
 
-You can set the :confval:`norecursedirs` option in an ini-file, for example your ``setup.cfg`` in the project root directory::
+You can set the :confval:`norecursedirs` option in an ini-file, for example your ``pytest.ini`` in the project root directory::
 
-    # content of setup.cfg
+    # content of pytest.ini
     [pytest]
     norecursedirs = .svn _build tmp*
 
@@ -94,8 +94,9 @@ You can configure different naming conventions by setting
 the :confval:`python_files`, :confval:`python_classes` and
 :confval:`python_functions` configuration options.  Example::
 
-    # content of setup.cfg
-    # can also be defined in in tox.ini or pytest.ini file
+    # content of pytest.ini
+    # can also be defined in in tox.ini or setup.cfg file, although the section
+    # name in setup.cfg files should be "tool:pytest"
     [pytest]
     python_files=check_*.py
     python_classes=Check
diff --git a/doc/en/goodpractices.rst b/doc/en/goodpractices.rst
index e1c4b0b5c..7c2fdccf2 100644
--- a/doc/en/goodpractices.rst
+++ b/doc/en/goodpractices.rst
@@ -196,6 +196,24 @@ required for calling the test command. You can also pass additional
 arguments to pytest such as your test directory or other
 options using ``--addopts``.
 
+You can also specify other pytest-ini options in your ``setup.cfg`` file
+by putting them into a ``[tool:pytest]`` section:
+
+.. code-block:: ini
+
+    [tool:pytest]
+    addopts = --verbose
+    python_files = testing/*/*.py
+
+
+.. note::
+    Prior to 3.0, the supported section name was ``[pytest]``. Due to how
+    this may collide with some distutils commands, the recommended
+    section name for ``setup.cfg`` files is now ``[tool:pytest]``.
+
+    Note that for ``pytest.ini`` and ``tox.ini`` files the section
+    name is ``[pytest]``.
+
 
 Manual Integration
 ^^^^^^^^^^^^^^^^^^
diff --git a/doc/en/xdist.rst b/doc/en/xdist.rst
index fa662b7d3..a33a1525a 100644
--- a/doc/en/xdist.rst
+++ b/doc/en/xdist.rst
@@ -90,7 +90,7 @@ and ``pytest`` will run your tests. Assuming you have failures it will then
 wait for file changes and re-run the failing test set.  File changes are detected by looking at ``looponfailingroots`` root directories and all of their contents (recursively).  If the default for this value does not work for you you
 can change it in your project by setting a configuration option::
 
-    # content of a pytest.ini, setup.cfg or tox.ini file
+    # content of a pytest.ini or tox.ini file
     [pytest]
     looponfailroots = mypkg testdir
 
@@ -181,7 +181,7 @@ to run tests in each of the environments.
 Specifying "rsync" dirs in an ini-file
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
-In a ``tox.ini`` or ``setup.cfg`` file in your root project directory
+In a ``pytest.ini`` or ``tox.ini`` file in your root project directory
 you may specify directories to include or to exclude in synchronisation::
 
     [pytest]
diff --git a/testing/deprecated_test.py b/testing/deprecated_test.py
index 87869bcf2..e610458e0 100644
--- a/testing/deprecated_test.py
+++ b/testing/deprecated_test.py
@@ -34,6 +34,15 @@ def test_funcarg_prefix_deprecation(testdir):
     ])
 
 
+def test_pytest_setup_cfg_deprecated(testdir):
+    testdir.makefile('.cfg', setup='''
+        [pytest]
+        addopts = --verbose
+    ''')
+    result = testdir.runpytest()
+    result.stdout.fnmatch_lines(['*pytest*section in setup.cfg files is deprecated*use*tool:pytest*instead*'])
+
+
 def test_str_args_deprecated(tmpdir, testdir):
     """Deprecate passing strings to pytest.main(). Scheduled for removal in pytest-4.0."""
     from _pytest.main import EXIT_NOTESTSCOLLECTED
diff --git a/testing/test_config.py b/testing/test_config.py
index 3ceb9cd70..dc7db6fd2 100644
--- a/testing/test_config.py
+++ b/testing/test_config.py
@@ -5,24 +5,28 @@ from _pytest.config import getcfg, get_common_ancestor, determine_setup
 from _pytest.main import EXIT_NOTESTSCOLLECTED
 
 class TestParseIni:
-    def test_getcfg_and_config(self, testdir, tmpdir):
+
+    @pytest.mark.parametrize('section, filename',
+                             [('pytest', 'pytest.ini'), ('tool:pytest', 'setup.cfg')])
+    def test_getcfg_and_config(self, testdir, tmpdir, section, filename):
         sub = tmpdir.mkdir("sub")
         sub.chdir()
-        tmpdir.join("setup.cfg").write(_pytest._code.Source("""
-            [pytest]
+        tmpdir.join(filename).write(_pytest._code.Source("""
+            [{section}]
             name = value
-        """))
-        rootdir, inifile, cfg = getcfg([sub], ["setup.cfg"])
+        """.format(section=section)))
+        rootdir, inifile, cfg = getcfg([sub])
         assert cfg['name'] == "value"
         config = testdir.parseconfigure(sub)
         assert config.inicfg['name'] == 'value'
 
-    def test_getcfg_empty_path(self, tmpdir):
-        getcfg([''], ['setup.cfg']) #happens on pytest ""
+    def test_getcfg_empty_path(self):
+        """correctly handle zero length arguments (a la pytest '')"""
+        getcfg([''])
 
     def test_append_parse_args(self, testdir, tmpdir, monkeypatch):
         monkeypatch.setenv('PYTEST_ADDOPTS', '--color no -rs --tb="short"')
-        tmpdir.join("setup.cfg").write(_pytest._code.Source("""
+        tmpdir.join("pytest.ini").write(_pytest._code.Source("""
             [pytest]
             addopts = --verbose
         """))
@@ -31,10 +35,6 @@ class TestParseIni:
         assert config.option.reportchars == 's'
         assert config.option.tbstyle == 'short'
         assert config.option.verbose
-        #config = testdir.Config()
-        #args = [tmpdir,]
-        #config._preparse(args, addopts=False)
-        #assert len(args) == 1
 
     def test_tox_ini_wrong_version(self, testdir):
         testdir.makefile('.ini', tox="""
@@ -47,12 +47,16 @@ class TestParseIni:
             "*tox.ini:2*requires*9.0*actual*"
         ])
 
-    @pytest.mark.parametrize("name", "setup.cfg tox.ini pytest.ini".split())
-    def test_ini_names(self, testdir, name):
+    @pytest.mark.parametrize("section, name", [
+        ('tool:pytest', 'setup.cfg'),
+        ('pytest', 'tox.ini'),
+        ('pytest', 'pytest.ini')],
+    )
+    def test_ini_names(self, testdir, name, section):
         testdir.tmpdir.join(name).write(py.std.textwrap.dedent("""
-            [pytest]
+            [{section}]
             minversion = 1.0
-        """))
+        """.format(section=section)))
         config = testdir.parseconfig()
         assert config.getini("minversion") == "1.0"