I was diagnosed with crohns in January of 2007. I had been on birth control for years and years but stopped taking it in December because I was sooo sick. In my head there was no sense in taking it if I was throwing everything back up. Plus, I thought maybe that was affecting it. Anyway, I was in the hospital for a week (that's when I FINALLY got diagnosed) and my last period was in December. It took until the middle of February to get my period back. And now I'm back on the pill, so I am "regular" again. But I do think that the stress on your body does play a part it in all. I did ask both the GI and my general practitioner who also does my exams. If you are really that concerned you could make an appointment with the OBGYN.