diff --git a/cython/setup.py.in b/cython/setup.py.in
index a4c96f1b8..0c37cd660 100644
--- a/cython/setup.py.in
+++ b/cython/setup.py.in
@@ -1,10 +1,19 @@
 import os
+import sys
 try:
     from setuptools import setup, find_packages
 except ImportError:
     from distutils.core import setup, find_packages
 
 
+script_path = os.path.abspath(os.path.realpath(__file__))
+install_path = os.path.abspath(os.path.realpath(os.path.join('${GTSAM_CYTHON_INSTALL_PATH}', 'setup.py')))
+if script_path != install_path:
+    print('setup.py is being run from an unexpected location: "{script_path}"')
+    print('please run `make install` and run the script from there')
+    sys.exit(1)
+
+
 packages = find_packages()
 
 setup(