Was treated for chlamydia two weeks ago and have had an upset stomach and stools of mostly mucus since what is wrong?

Antibiotics : The antibiotics can kill off good bacteria in your intestines. Probiotics can help but if you see blood in your bowel movement or your symptoms get worst you need to be seen immediately since these can be symptoms of a serious side effect of antibiotics called pseudomembranous colitis caused by clostridium difficle.

Mucusy stools: Certain antibiotics may cause colitis due to changes in the colon flora. (good bacteria vs. opportunistic bacteria) On of these bacteria is c. dificile which produces a toxin that may cause severe colitis. Please check with our primary care doctor and ask to submit some stool samples to check for this condition. In the meantime, you may want to try a probiotic called "FLOASTOR" twice daily.

Probiotics: Could be a problem with your gut flora killed by the antibiotics. Eat yogurt like Activia with friendly Bifidobacterium and take Acidophillus OTC. Prebiotics, which contain nondigestible carbohydrates ,found in whole grains, onions, garlic, leeks, artichokes, asparagus, and chicory root will also help. Give the process a few weeks.

Abnl GU flora : The antibiotics have likely effected the bacterial flora in your GU system. Doing probiotics, like eating yogurt, should help. If it doesn't get better, you need to see you MD to make sure you don't have an infection (i.e. C Dificile)