In the fall of 2001, approximately 15,000 U.S. military personnel participated in a military exercise in the northwestern Egyptian desert. To assess the prevalence and impact of diarrhea and enteropathogen distribution, we conducted a post-deployment survey and a case series study. A departure convenience sampling (n = 3725) was used in the post-deployment survey. Overall, 9.3% reported diarrhea, 2.6% sought medical care, and 2.8% stopped or decreased their work for at least a day. Among those reporting diarrhea, 41.7% had symptoms for less than 2 days, 43.5% had symptoms from 2-5 days, and 14.8% had symptoms for more than 5 days. In the case series study, pathogens were identified in 53.6% of the 129 cases enrolled. Pathogens identified included enterotoxigenic E. coli (n = 53), enteroaggregative E. coli (n = 13), Cryptosporidium (n = 9), Campylobacter jejuni (n = 7), noroviruses (n = 7), Shigella flexneri (n = 2), rotavirus (n = 2), and Entamoeba histolytica (n = 2). Among those seeking care for diarrhea, two thirds reported a decreased ability or inability to perform their jobs for at least one day, but overall, diarrhea was much less prevalent than in past surveys in this region, with minimal impact on the mission.