Could be low electrolytes - potassium, magnesium, sodium, etc. Try a sports drink, tomato juice or maybe coconut water afterward and see what happens.

I find that running can make you very regular - i.e. make you have to poop more often. Not sure why, but other runners I know have said the same thing.

Also, weird question. Are you eating enough to support the higher activity level of your running? Could it be hunger? I know, stupid/obvious question, but some of the women I know really don't eat enough to support heavy exercise without starving themselves. (I never have that problem. Ever. )

I gave up dairy altogether and stopped having post run stomach problems.

Are you eating enough potassium - try bananas a few hours before you run

Every time I run, I have horrendous stomach aches for the next day or two. I've tried not eating dairy before running, staying well hydrated, etc. but nothing seems to help. Has anyone else experienced this? Any suggestions? I love running and don't want to stop, but the stomach aches are awful.