Ask your doctor about Celiac disease. It is an intolerance of gluten (mainly from wheat products). It is greatly under-diagnosed.

The definitive diagnosis is with a biopsy from the intestines, but if the symptoms continue a three or four day regimen of gluten-free eating can tell a lot. If you are symptom free after the gluten-free days, then you definitely want the biopsy done, as gluten-free eating is a huge burden.

See: Celiac Disease Foundation

Also see: http://en.wikipedia.org/wiki/Coeliac_disease