Enterotoxigenic strains of Bacteriodes fragilis (ETBF) have recently been found to be associated with diarrheal illness in Apache and Bangladeshi children. This study was conducted to define the role of ETBF in diarrhea of children in an urban setting. Fecal specimens from 991 children with diarrhea and 581 asymptomatic age-matched controls were cultured for B. fragilis (BF). The isolates were tested for enterotoxin production using a human colonic epithelial cell line. BF was isolated from 318 (32.1%) of the patients and 123 (21.2%) of the controls (p < 0.001). In children < 1 year old which comprised about 50% of both patients and controls, the BF isolation rates were comparable (26.5% vs 25.7%; p = 0.812), contrasting with the significant difference in isolation rates for children > or = 1 year (37.6% vs 16.5%; p = < 0.001). Overall, ETBF were identified in 4.4% of patients and 3.1% of controls (p = 0.2). However, ETBF were significantly associated with diarrheal disease in children 1-5 years (5.4% vs 1.8%; p = 0.033) and 1-10 years (4.8% vs 1.5%; p = 0.021) in age. ETBF were isolated the year round and comprised 14.4% and 15% of the BF isolated from the patients and controls, respectively, suggesting that part of the indigenous BF are inherently enterotoxin producers. In this study, BF and ETBF were associated with diarrheal illness in children 1-10 years old.