A Salmonella Enteritidis (SE) outbreak in Japan was investigated with an observational study, analytical epidemiology and bacteriological examination (including phage typing). The outbreak occurred among 96 schoolchildren, and was caused by SE phage type 1. The outbreak source was dessert buns served at a school lunch (RR 42·55, 95% CI 5·93–305·11, P<0·001). The buns were probably cross-contaminated from eggs from a factory with a history of SE-contaminated products. The incubation period was longer than usual (3–16 days, median 8 days). A low contaminating dose may account for the long incubation period and low attack rate. Outbreak detection was hampered by the absence of routine Salmonella surveillance in Japan. The investigation was complicated by concurrent illnesses from other SE phage types. It was successful, in part, because adequate food samples were available for microbiological testing.