diff --git a/changelog/3773.bugfix.rst b/changelog/3773.bugfix.rst
new file mode 100644
index 000000000..427f6c274
--- /dev/null
+++ b/changelog/3773.bugfix.rst
@@ -0,0 +1 @@
+Fix collection of tests from ``__init__.py`` files if they match the ``python_files`` configuration option.
diff --git a/src/_pytest/pytester.py b/src/_pytest/pytester.py
index 2372ea663..4ba428cd8 100644
--- a/src/_pytest/pytester.py
+++ b/src/_pytest/pytester.py
@@ -672,7 +672,9 @@ class Testdir(object):
             example_path.copy(result)
             return result
         else:
-            raise LookupError("example is not found as a file or directory")
+            raise LookupError(
+                'example "{}" is not found as a file or directory'.format(example_path)
+            )
 
     Session = Session
 
diff --git a/src/_pytest/python.py b/src/_pytest/python.py
index 7fb7ff9ef..977b07442 100644
--- a/src/_pytest/python.py
+++ b/src/_pytest/python.py
@@ -201,15 +201,19 @@ def pytest_collect_file(path, parent):
     ext = path.ext
     if ext == ".py":
         if not parent.session.isinitpath(path):
-            for pat in parent.config.getini("python_files") + ["__init__.py"]:
-                if path.fnmatch(pat):
-                    break
-            else:
+            if not path_matches_patterns(
+                path, parent.config.getini("python_files") + ["__init__.py"]
+            ):
                 return
         ihook = parent.session.gethookproxy(path)
         return ihook.pytest_pycollect_makemodule(path=path, parent=parent)
 
 
+def path_matches_patterns(path, patterns):
+    """Returns True if the given py.path.local matches one of the patterns in the list of globs given"""
+    return any(path.fnmatch(pattern) for pattern in patterns)
+
+
 def pytest_pycollect_makemodule(path, parent):
     if path.basename == "__init__.py":
         return Package(path, parent)
@@ -590,6 +594,11 @@ class Package(Module):
                 self.session.config.pluginmanager._duplicatepaths.remove(path)
 
         this_path = self.fspath.dirpath()
+        init_module = this_path.join("__init__.py")
+        if init_module.check(file=1) and path_matches_patterns(
+            init_module, self.config.getini("python_files")
+        ):
+            yield Module(init_module, self)
         pkg_prefixes = set()
         for path in this_path.visit(rec=self._recurse, bf=True, sort=True):
             # we will visit our own __init__.py file, in which case we skip it
diff --git a/testing/example_scripts/collect/collect_init_tests/pytest.ini b/testing/example_scripts/collect/collect_init_tests/pytest.ini
new file mode 100644
index 000000000..7c4795540
--- /dev/null
+++ b/testing/example_scripts/collect/collect_init_tests/pytest.ini
@@ -0,0 +1,2 @@
+[pytest]
+python_files = *.py
diff --git a/testing/example_scripts/collect/collect_init_tests/tests/__init__.py b/testing/example_scripts/collect/collect_init_tests/tests/__init__.py
new file mode 100644
index 000000000..9cd366295
--- /dev/null
+++ b/testing/example_scripts/collect/collect_init_tests/tests/__init__.py
@@ -0,0 +1,2 @@
+def test_init():
+    pass
diff --git a/testing/example_scripts/collect/collect_init_tests/tests/test_foo.py b/testing/example_scripts/collect/collect_init_tests/tests/test_foo.py
new file mode 100644
index 000000000..8f2d73cfa
--- /dev/null
+++ b/testing/example_scripts/collect/collect_init_tests/tests/test_foo.py
@@ -0,0 +1,2 @@
+def test_foo():
+    pass
diff --git a/testing/test_collection.py b/testing/test_collection.py
index ce0e3a920..fb3860f99 100644
--- a/testing/test_collection.py
+++ b/testing/test_collection.py
@@ -938,3 +938,17 @@ def test_fixture_scope_sibling_conftests(testdir):
             "*1 passed, 1 error*",
         ]
     )
+
+
+def test_collect_init_tests(testdir):
+    """Check that we collect files from __init__.py files when they patch the 'python_files' (#3773)"""
+    p = testdir.copy_example("collect/collect_init_tests")
+    result = testdir.runpytest(p, "--collect-only")
+    result.stdout.fnmatch_lines(
+        [
+            "*<Module '__init__.py'>",
+            "*<Function 'test_init'>",
+            "*<Module 'test_foo.py'>",
+            "*<Function 'test_foo'>",
+        ]
+    )