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Gastrointestinal Causes of Yellow Diarrhea. There are a few disorders of the stomach and bowel which can cause yellow diarrhea. It can be quite complicated to make a diagnosis as the symptoms can overlap, therefore if you develop yellow diarrhea and you have other symptoms you should see a doctor and have some tests done.
1 Malabsorption syndromes are another common cause of watery stool or watery diarrhea. 2  In these cases, there is failure of the small intestine to absorb nutrients, which is further compounded by decreased water absorption in the large intestine. Chronic cases of infectious diarrhea may be seen in immunocompromised patients (as seen in HIV diarrhea) or associated with a Clostridium difficile infection (as seen in antibiotic-associated diarrhea). 2  Malabsorption syndromes are another common cause of watery stool or watery diarrhea.