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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.
A few of the more common causes of acute diarrhea include: 1  Viral infections, such as the stomach flu. 2  Bacterial infections, such as those involving Salmonella typhi or E. coli. 3  Parasites, such as Giardia. 4  Medicines, such as antibiotics. 5  Anxiety.