Bacterial proliferation in the small intestine can induce the protraction of diarrhea due to malabsorption of the nutrients. We performed the culture of the small intestine juice for the aerobic and anaerobic flora in 40 infants with persistent and acute diarrhea. Bacterial proliferation was observed in 32 (80%) patients, being 30 (75%) due to the aerobic microflora and 17 (43%) due to the anaerobic microflora. There was no statistical difference in the bacterial growth between acute and persistent diarrhea. The aerobic bacteria most frequently isolated was E. coli in 23 patients, and Bacteroides sp was the most prevalent anaerobic bacteria, isolated in 9 cases. The transitory flora was significantly more abundant in patients with persistent diarrhea.