Dear all, As suggested in this github issue ( https://github.com/scipy/scipy/issues/3870), I would like to discuss the merit of introducing a new function nanpdist into scipy.spatial. I have also brought up the problem in the following previous e-mail ( http://comments.gmane.org/gmane.comp.python.scientific.devel/18956) and on SO ( http://stackoverflow.com/questions/24781461/compute-the-pairwise-distance-in... ). Warren suggested three ways to tackle this problem: 1. Don't change anything--the users should clean up their data! 2. nanpdist 3. Add a keyword argument to pdist that determines how nan should be treated. Clearly, I don't favor the first option since I believe missing values can be important pieces of information, too. I slightly tend towards option two because adding a keyword will further complicate an already very long pdist function. I'm happy to submit a pull request if there is a consensus that something should be done. Best, Moritz