Bacteria and viruses - infectious agents - (the most common cause) are the most frequent causes of gastroenteritis worldwide. Infections cause diarrhea and other symptoms by causing inflammation of the gastrointestinal (GI) tissue. The infections increase the fluid content in the intestines and colon by changing the gastrointestinal tract's ability to absorb water and by increasing the speed of transit (motility) for things you ingest. This, in turn, causes diarrhea. Infectious agents may physically damage intestinal cells directly or indirectly with secreted toxins.

Viral causes of stomach flu
The most prevalent cause of gastroenteritis is Norovirus. It causes about 50% to 70% of viral gastroenteritis cases, while Rotavirus, Astrovirus, Adenovirus, and Sapovirus strains cause most of the other viral gastroenteritis infections. Norovirus also was listed as the leading cause of gastroenteritis in children under 5 years old.

Bacterial causes of stomach flu
Bacterial causes of gastroenteritis that occur worldwide are Salmonella, Shigella, Campylobacter Aeromonas, and Escherichia coli (E. coli) strains of bacteria. Other bacteria like Clostridium, Vibrio, Campylobacter, and Yersinia spp can cause outbreaks occasionally. Occasionally, some bacterial causes of gastroenteritis (for example, Salmonella and , certain E. coli strains) may produce hemorrhagic or bloody diarrhea.

Parasitic causes of stomach flu
Parasites such as Giardia, Cryptosporidium, and Entamoeba infections can cause gastroenteritis and occasionally, other parasites have outbreaks such as the Cyclospora outbreak.