Two U.S. Navy ships experienced outbreaks of gastroenteritis following port visits to Southeast Asia during August to September 1999. The USS Peleliu (LHA 5) had 162 (6% attack rate) medical visits and the USS Constellation (CV 64) had 425 medical visits (9% attack rate). Navy Environmental and Preventive Medicine Unit No. 5 personnel conducted on-board molecular diagnostic assays to presumptively detect the presence of genogroup I Norwalk-like viruses (NLV) in both outbreaks. NLV RNA were detected in 4 (80%) of 5 Peleliu stool specimens and in 9 (36%) of 25 from the Constellation. Significant antibody titer rises to NLV antigens were measured in 18 (62%) of 29 Peleliu and 69 (68%) of 102 Constellation cases, but only in 1 (4%) of 28 asymptomatic controls. All environmental swipes were negative for NLV. Stools yielded no bacterial or parasitic enteropathogens. No point source was found for either ship. The on-site laboratory investigation can provide important information for outbreak control and prevention while new cases are still presenting.