PEP 250 suggests changing the sitedirs setup in site.py from sitedirs = [prefix] to sitedirs == [makepath(prefix, "lib", "site-packages")] on windows. it then goes on to say that This change does not preclude packages using the current location -- the change only adds a directory to sys.path, it does not remove anything. this isn't true (even after correcting the typo), since the sitedirs list isn't only added to the path; it's also used to look for PTH files. after this change, PTH files located under prefix will no longer be found. the following change works a bit better: sitedirs = [prefix, makepath(prefix, "lib", "site-packages")] Cheers /F