The flagellated parasitic protozoan Hexamita salmonis were found in the upper intestine and pyloric caeca in large numbers in the farmed rainbow trout fry. Generally, infected fish fry showed significant level of mortality, exophthalmia and abdominal distension. Histopathologicaly, invasion of the pyloric caeca or upper intestine epithelium by the parasites and severe necrotizing of enteric mucosal epithelium and perforation of the serosal surface was observed. Inflammatory response was generally lacking in the gut wall, but large granulomatous lesions in some perforated area were found. In the histological sections, characteristic paired anterior nuclei of the parasites were easily recognized.