In April of 2003, an outbreak of gastroenteritis was reported in a training command (Centro de Instrucción Técnica y Entrenamiento Naval (CITEN)) at a Peruvian naval base located near Lima, Peru. The Naval Medical Research Center Detachment, in collaboration with the National Peruvian Naval Hospital, conducted an investigation to determine the causative agent and potential source of the outbreak. Between April 3 and 5, 172 (16%) of 1,092 military trainees reported to the CITEN clinic with diarrhea. Of 74 trainees for whom bacterial cultures were performed, Shigella spp. were isolated from 5 (6.8%), Campylobacter spp. from 5 (6.8%), and enterotoxigenic Escherichia coli from 2 (2.7%). Pathogenic parasites were identified in 22 of 64 (34%) trainees for whom microscopic observation for ova and parasites was performed. Stool samples from asymptomatic controls could not be collected, thus we were unable to confirm that the enteropathogens isolated were the etiologic agent(s). Several food items and the hands of food handlers were contaminated with coliform bacteria and drinking water was not adequately chlorinated. Preventative measures have since reduced the number of diarrhea cases at the CITEN.