diff --git a/_pytest/config.py b/_pytest/config.py
index 06214e6ca..54efdde1f 100644
--- a/_pytest/config.py
+++ b/_pytest/config.py
@@ -1329,10 +1329,14 @@ def determine_setup(inifile, args, warnfunc=None, rootdir_cmd_arg=None):
     if inifile:
         iniconfig = py.iniconfig.IniConfig(inifile)
         is_cfg_file = str(inifile).endswith('.cfg')
+        # TODO: [pytest] section in *.cfg files is depricated. Need refactoring.
         sections = ['tool:pytest', 'pytest'] if is_cfg_file else ['pytest']
         for section in sections:
             try:
                 inicfg = iniconfig[section]
+                if is_cfg_file and section == 'pytest' and warnfunc:
+                    from _pytest.deprecated import SETUP_CFG_PYTEST
+                    warnfunc('C1', SETUP_CFG_PYTEST.replace('setup.cfg', str(inifile)))
                 break
             except KeyError:
                 inicfg = None
diff --git a/testing/deprecated_test.py b/testing/deprecated_test.py
index 92ec029d4..77e0e3893 100644
--- a/testing/deprecated_test.py
+++ b/testing/deprecated_test.py
@@ -48,6 +48,15 @@ def test_pytest_setup_cfg_deprecated(testdir):
     result.stdout.fnmatch_lines(['*pytest*section in setup.cfg files is deprecated*use*tool:pytest*instead*'])
 
 
+def test_pytest_custom_cfg_deprecated(testdir):
+    testdir.makefile('.cfg', custom='''
+        [pytest]
+        addopts = --verbose
+    ''')
+    result = testdir.runpytest("-c", "custom.cfg")
+    result.stdout.fnmatch_lines(['*pytest*section in custom.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