A health assessment survey was collected from US military personnel deployed to the Middle East taking part in the "Rest and Recuperation" program or on temporary assignment to Camp As Sayliyah Doha, Qatar, from January to December 2004. In addition, a concurrent clinic-based observational study was conducted to determine pathogen etiology and potential risk factors. From 28,322 health assessment surveys, overall self-reported incidence of diarrhea was 4.9 cases per 100 person-months. Disease incidence increased with rank and was higher in Iraq compared with Afghanistan. During this period, 109 US military personnel with acute diarrhea and 85 asymptomatic personnel were enrolled in the observational study. Enterotoxigenic E. coli (ETEC) was the predominant pathogen (32%), followed by enteroaggregative E. coli (12%) and Salmonella spp. (6%). These data are consistent with previous reports implicating ETEC as the primary cause of acute diarrhea for military personnel deployed to this region.