A hospital-based case-control study including 92 children with diarrhea for longer than 14 days and 92 controls without gastrointestinal symptoms was performed to describe the association between the excretion of enteric pathogens and persistent diarrhea. In patients the most frequently isolated stool pathogens were enteroaggregative Escherichia coli (19.6%), nontyphoidal Salmonella spp. (17.4%), E. coli with diffuse adherence pattern (7.6%), G. lamblia (7.6%) and enterotoxigenic E. coli (5.4%). The excretion rates in patients were significantly greater than in controls only for nontyphoidal Salmonella spp. (P = 0.0006) and enteroaggregative E. coli (P = 0.016).