Hey Thomas and Vinay, thanks for looking into this. Although I discovered this problem on my MacOS laptop 6 months ago, today I also reproduced this issue on my Ubuntu desktop.

```
/home/mhaase/Downloads $ mkdir temp
/home/mhaase/Downloads $ cd temp
/home/mhaase/Downloads/temp $ pyvenv --system-site-packages pyvenv
/home/mhaase/Downloads/temp $ source pyvenv/bin/activate
(pyvenv) /home/mhaase/Downloads/temp $ pip --version
pip 9.0.1 from /usr/local/lib/python2.7/dist-packages (python 2.7)
(pyvenv) /home/mhaase/Downloads/temp $ python --version
Python 3.5.2
(pyvenv) /home/mhaase/Downloads/temp $ cat /etc/lsb-release 
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=16.04
DISTRIB_CODENAME=xenial
DISTRIB_DESCRIPTION="Ubuntu 16.04.1 LTS"
(pyvenv) /home/mhaase/Downloads/temp $ uname -av
Linux prodigy 4.4.0-57-generic #78-Ubuntu SMP Fri Dec 9 23:50:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
```

This bug is really annoying if you work with scientific Python (numpy, scipy, sklearn), as those are big, stable packages that I would prefer to install once on my system and then access from multiple venvs. The standardization of linux wheels in 2016 made this slightly less problematic (don't need to compile all of numpy just to create a venv for an ipython notebook), but this is still an annoying bug. Unfortunately, I think it lacks the upvotes to get attention from the PyPA developers.

Maybe it would help to post this on the https://groups.google.com/forum/#!forum/pypa-dev mailing list?