Hi, Babies who are breast fed rarely have diarrhea. A common cause of watery diarrhea in young infants is gastroenteritis due to a virus. The virus causes inflammation of the inside lining of the small intestine. This causes loss of the chemical that is normally on the intestinal lining that breaks down the sugar(lactose) that is in regular milk-based formula. This sugar then is carried out the intestinal tract pulling water with it. The results are frequent, watery stools. Another cause could be cow s milk allergy. His doctors have most likely already obtained stool specimens to look for infections. Soybean-based formula does not contain lactose and many parents offer this instead of milk-based formula when infant has diarrhea. I am uncomfortable in suggesting medicines to treat infantile diarrhea because of the concern for side effects. Hope I have answered your query. Let me know if I can assist you further.