diff --git a/mypy/main.py b/mypy/main.py
index a36bb30b293f..95f420b5f9a2 100644
--- a/mypy/main.py
+++ b/mypy/main.py
@@ -1051,11 +1051,10 @@ def set_strict_flags() -> None:
     # Set target.
     if special_opts.modules + special_opts.packages:
         options.build_type = BuildType.MODULE
-        search_dirs = get_search_dirs(options.python_executable)
-        search_paths = SearchPaths((os.getcwd(),),
-                                   tuple(mypy_path() + options.mypy_path),
-                                   tuple(search_dirs),
-                                   ())
+        sys_path, _ = get_search_dirs(options.python_executable)
+        search_paths = SearchPaths(
+            (os.getcwd(),), tuple(mypy_path() + options.mypy_path), tuple(sys_path), ()
+        )
         targets = []
         # TODO: use the same cache that the BuildManager will
         cache = FindModuleCache(search_paths, fscache, options)
diff --git a/mypy/modulefinder.py b/mypy/modulefinder.py
index 232154664772..c9e3d058ffbd 100644
--- a/mypy/modulefinder.py
+++ b/mypy/modulefinder.py
@@ -723,7 +723,7 @@ def default_lib_path(data_dir: str,
 
 
 @functools.lru_cache(maxsize=None)
-def get_search_dirs(python_executable: Optional[str]) -> List[str]:
+def get_search_dirs(python_executable: Optional[str]) -> Tuple[List[str], List[str]]:
     """Find package directories for given python.
 
     This runs a subprocess call, which generates a list of the directories in sys.path.
@@ -732,15 +732,15 @@ def get_search_dirs(python_executable: Optional[str]) -> List[str]:
     """
 
     if python_executable is None:
-        return []
+        return ([], [])
     elif python_executable == sys.executable:
         # Use running Python's package dirs
-        sys_path = pyinfo.getsearchdirs()
+        sys_path, site_packages = pyinfo.getsearchdirs()
     else:
         # Use subprocess to get the package directory of given Python
         # executable
         try:
-            sys_path = ast.literal_eval(
+            sys_path, site_packages = ast.literal_eval(
                 subprocess.check_output([python_executable, pyinfo.__file__, 'getsearchdirs'],
                 stderr=subprocess.PIPE).decode())
         except OSError as err:
@@ -748,7 +748,7 @@ def get_search_dirs(python_executable: Optional[str]) -> List[str]:
             raise CompileError(
                 [f"mypy: Invalid python executable '{python_executable}': {reason}"]
             ) from err
-    return sys_path
+    return sys_path, site_packages
 
 
 def add_py2_mypypath_entries(mypypath: List[str]) -> List[str]:
@@ -837,22 +837,26 @@ def compute_search_paths(sources: List[BuildSource],
     if options.python_version[0] == 2:
         mypypath = add_py2_mypypath_entries(mypypath)
 
-    search_dirs = get_search_dirs(options.python_executable)
-    for search_dir in search_dirs:
-        assert search_dir not in lib_path
-        if (search_dir in mypypath or
-                any(p.startswith(search_dir + os.path.sep) for p in mypypath) or
-                (os.path.altsep
-                    and any(p.startswith(search_dir + os.path.altsep) for p in mypypath))):
-            print(f"{search_dir} is in the MYPYPATH. Please remove it.", file=sys.stderr)
+    sys_path, site_packages = get_search_dirs(options.python_executable)
+    # We only use site packages for this check
+    for site in site_packages:
+        assert site not in lib_path
+        if (
+            site in mypypath
+            or any(p.startswith(site + os.path.sep) for p in mypypath)
+            or (os.path.altsep and any(p.startswith(site + os.path.altsep) for p in mypypath))
+        ):
+            print(f"{site} is in the MYPYPATH. Please remove it.", file=sys.stderr)
             print("See https://mypy.readthedocs.io/en/stable/running_mypy.html"
                   "#how-mypy-handles-imports for more info", file=sys.stderr)
             sys.exit(1)
 
-    return SearchPaths(python_path=tuple(reversed(python_path)),
-                       mypy_path=tuple(mypypath),
-                       package_path=tuple(search_dirs),
-                       typeshed_path=tuple(lib_path))
+    return SearchPaths(
+        python_path=tuple(reversed(python_path)),
+        mypy_path=tuple(mypypath),
+        package_path=tuple(sys_path + site_packages),
+        typeshed_path=tuple(lib_path),
+    )
 
 
 def load_stdlib_py_versions(custom_typeshed_dir: Optional[str]) -> StdlibVersions:
diff --git a/mypy/pyinfo.py b/mypy/pyinfo.py
index 1cd57c65665c..ed0fed370700 100644
--- a/mypy/pyinfo.py
+++ b/mypy/pyinfo.py
@@ -7,12 +7,13 @@
 possible.
 """
 import os
+import site
 import sys
 import sysconfig
 
 MYPY = False
 if MYPY:
-    from typing import List
+    from typing import Tuple, List
 
 if __name__ == '__main__':
     # HACK: We don't want to pick up mypy.types as the top-level types
@@ -24,7 +25,22 @@
     sys.path = old_sys_path
 
 
-def getsearchdirs():
+def getsitepackages():
+    # type: () -> List[str]
+    res = []
+    if hasattr(site, "getsitepackages"):
+        res.extend(site.getsitepackages())
+
+        if hasattr(site, "getusersitepackages") and site.ENABLE_USER_SITE:
+            res.insert(0, site.getusersitepackages())
+    else:
+        from distutils.sysconfig import get_python_lib
+
+        res = [get_python_lib()]
+    return res
+
+
+def getsyspath():
     # type: () -> List[str]
     # Do not include things from the standard library
     # because those should come from typeshed.
@@ -54,6 +70,14 @@ def getsearchdirs():
     return [p for p in abs_sys_path if p not in excludes]
 
 
+def getsearchdirs():
+    # type: () -> Tuple[List[str], List[str]]
+    return (
+        getsyspath(),
+        getsitepackages(),
+    )
+
+
 if __name__ == '__main__':
     if sys.argv[-1] == 'getsearchdirs':
         print(repr(getsearchdirs()))