OBJECTIVE The aim of this study was to investigate a large food-borne outbreak associated with eggs contaminated by Salmonella Enteritidis in a military unit using pulse field gel electrophoresis (PFGE) and the Repetitive-sequence-based PCR (rep-PCR) employing the DiversiLab system. MATERIALS AND METHODS In mid-January 2008, a food-borne outbreak associated with S. Enteritidis occurred in a military unit located in the city centre of Isparta. A total of 2,469 patients were registered to six hospitals with gastrointestinal disease symptoms such as diarrhea and abdominal pain. Of those registered, 445 were hospitalized. S. Enteritidis was isolated from 276 stool samples and a blood sample of the hospitalized patients and from a food item. The PFGE patterns after XbaI digestion and rep-PCR profiles produced by the DiversiLab system were determined for eight randomly selected stool isolates, one blood isolate and one food isolate. RESULTS The PFGE patterns of all isolates were identical. The Rep-PCR profiles produced by using the DiversiLab system showed that all isolates were indistinguishable. The PFGE and rep-PCR interpretations were concordant for the S. Enteritidis isolates. All stool isolates, one blood isolate and one food isolate were susceptible to all antibiotics tested. CONCLUSION This data suggest that the DiversiLab system may be a reasonable alternative to PFGE for investigation and control of S. Enteritidis outbreaks, since it is easy to use, rapid and does not require highly skilled operators.