diff --git a/mypy/build.py b/mypy/build.py
index a24a27bf2dae..783a10aad532 100644
--- a/mypy/build.py
+++ b/mypy/build.py
@@ -275,9 +275,21 @@ def compute_search_paths(sources: List[BuildSource],
     if alt_lib_path:
         mypypath.insert(0, alt_lib_path)
 
+    package_path = tuple(_get_site_packages_dirs(options.python_executable))
+    for site_dir in package_path:
+        assert site_dir not in lib_path
+        if site_dir in mypypath:
+            print("{} is in the MYPYPATH. Please remove it.".format(site_dir), file=sys.stderr)
+            sys.exit(1)
+        elif site_dir in python_path:
+            print("{} is in the PYTHONPATH. Please change directory"
+                  " so it is not.".format(site_dir),
+                  file=sys.stderr)
+            sys.exit(1)
+
     return SearchPaths(tuple(reversed(python_path)),
                        tuple(mypypath),
-                       tuple(_get_site_packages_dirs(options.python_executable)),
+                       package_path,
                        tuple(lib_path))