Emerging or reemerging infections due to bacterial disease may be a local, regional or global problem. Bacterial acute gastroenteritis is a potential cause of substantial morbidity in travelers and deployed U.S. military personnel. A surveillance study was conducted over a two-year period in Indonesia among 6760 patients with debilitating diarrheal diseases. Of the 6,760 patients, 587 (9%) of the patient stools were positive for bacteria. The proportions of bacteria isolated from the 587 patients were: Shigella flexneri (39%), Salmonella spp. (26%), Vibrio spp. (17%), S. sonnei (7%), Campylobacter jejuni (4.4%), Salmonella typhi (3%) and S. dysenteriae (2.3%). Shigella flexneri was the most prevalent pathogen isolated, over Vibrio spp. No V. cholerae was isolated in the cities of Pontianak, Padang or Batam in Indonesia. Shigella dysenteriae reemergence was noted in Bali, Kalimantan, Batam and Jakarta after an absence of 15 years. Isolation of a high proportion of S. flexneri, and Vibrio spp. occurred during the rainy months. All bacterial isolates were susceptible to quinolones, with the exception of C. jejuni and Salmonella spp., which were resistant to ciprofloxacin, norfloxacin and nalidixic acid. Our findings highlight the decline of V. cholerae, the rise of S. flexneri and the reemergence of S. dysenteriae in Indonesia. The study also documents the emergence of quinolone-resistant Campylobacter spp. in the Indonesia archipelago.