I, too, have PCOS... and suffer from IBS. All I can tell you is to give it some time- and try taking some fiber. My stomach was a complete mess the first week and a half of Atkins (many people on here are commenting about being constipated - well, not me!! I was just the opposite ). However, around day 10 or so my system started to adjust... and now I feel much, much better than I have in a long time.