The etiology of the protracted diarrhea is ill-defined, but in the underdeveloped countries acute gastroenteritis might be the most common triggering factor, especially due to certain enteropathogenic bacteria, such as enteropathogenic E. coli (EPEC) and Salmonella. We investigated the role of these agents in the genesis of protracted diarrhea in 29 infants with a mean age of 4.6 months. The patients underwent the following tests: stool culture, culture of the jejunal secretion, and small bowel and rectal biopsies. The stool culture was positive for some enteropathogenic bacteria in 17 (58.6%) patients: EPEC serotypes 0126, 0125, 055, 026, 0111, 0127, 0114, 0158, and 0119 and Salmonella were identified. The jejunal secretion culture revealed bacterial proliferation in 15 (51.7%) patients, and the following bacteria were isolated: EPEC 0142, Proteus, Klebsiella, Enterobacter, EPEC 0114, Pseudomonas, EPEC 0111, Salmonella, and EPEC 0119. The small bowel biopsy showed subtotal villous atrophy in 13 (44.8%) patients, and the rectal biopsy revealed colitis in 13 (44.8%) patients. These findings stress the importance of those enteropathogenic bacteria in the genesis of protracted diarrhea in underdeveloped countries mainly due to food intolerance leading to aggravation of the nutritional status.