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We investigated the etiology of acute diarrhea among Peruvian military recruits undergoing three months of basic combat training near the Amazonian city of Iquitos. From January through September 2002, 307 of 967 recruits were seen at the Health Post for diarrhea (attack rate [AR] = 31.8%, incidence = 1.28 95% confidence interval [CI] = 1.14–1.43] episodes/person-year). Shigella spp. were the most common bacterial pathogen recovered from recruits experiencing diarrhea episodes. These bacteria were isolated from 89 (40%) of 225 diarrheal stools examined (AR = 7.6%, incidence = 0.30 [95% CI = 0.24–0.38] episodes/person-year). Most (83 of 90; 92%) of the Shigella isolates were S. flexneri, of which 57 (69%) were serotype 2a. Seventy-six percent of Shigella isolates were resistant to sulfamethoxazole/trimethoprim and all were sensitive to ciprofloxacin. Peruvian soldiers may be an excellent population in which to test the efficacy of S. flexneri vaccines in advanced development.