BACKGROUND Over a period of 4 days between May 18-21, 1998, a multifocal outbreak of diarrhea, involving 175 Israel Defence Force soldiers and at least 54 civilians, occurred in the Golan Heights. METHODS Stool samples from 40 affected soldiers were collected for microbiological testing. In addition, a rapid PCR technique was employed for the direct detection of the heat-labile (LT) and heat-stable toxin (ST) genes of enterotoxigenic Escherichia coli (ETEC) in stool samples. RESULTS All 40 stool specimens taken from patients with diarrhea was negative by culture. However, ETEC was detected in 16 stool specimens using the rapid PCR method. The epidemiological investigation found no association between the food items consumed prior to the onset of the outbreak and the attack rate of diarrhea. A review of the water distribution system revealed that all affected military posts and civilian communities were supplied by a common water pipeline. Water sampled from various points along the distribution system showed inadequate chlorination and high concentrations of E. coli. CONCLUSIONS This report suggests that the involvement of ETEC in the etiology of waterborne diarrheal outbreaks may be underestimated, probably due to the difficulties involved in the laboratory identification of this enteropathogen. Adoption of our rapid method for the identification of ETEC, which is applicable to routine diagnostic laboratories, facilitates pathogen detection within hours, and allows early intervention in cases of widespread diarrheal epidemics.