Can taking antibiotics cause my child to have loose stools?

This is not an allergic reaction to the medicine. Diarrhea and mild abdominal pain are two of the most common side effects of antibiotics. In addition, the loose stools may just be part of the original illness. As long as you keep your child hydrated by giving plenty of fluids, the loose stools shouldn’t cause any harm (although you may have to treat a diaper rash). The diarrhea will likely stop soon after the antibiotic course is completed and the illness is over. Do not stop the antibiotic without calling your pediatrician first. Some physicians now suggest giving yogurt with live cultures or probiotics to help replace the good gut bacteria that antibiotics can wipe out.