With the improved therapy for acute diarrhea, persistent diarrhea (> 14 days) is emerging as a major problem in developing countries. However, the etiologies and pathogenesis of persistent diarrhea remain poorly understood. We conducted a prospective case-control study in children < 3 years old presenting to the hospital with persistent diarrhea in Fortaleza, Brazil. Over the study period (August 1988 to March 1991), 56 children seen with persistent diarrhea, 52 children seen with acute diarrhea, and 42 controls attending the same hospital/clinic for illnesses other than diarrhea were enrolled. A potential pathogen was found in 91% of children with persistent diarrhea and 90% of those with acute diarrhea versus 45% of controls (both p's < 0.01). Thirty-four percent of persistent (19/56) and 38% of acute (20/52) diarrhea cases versus 2% (1/42) of controls (both p's < 0.01) had multiple pathogens. Enteroaggregative Escherichia coli (EAggEC) were found in 68% (38/56) of children with persistent diarrhea versus 31% (13/42) of controls (p < 0.01) and in 46% (24/52) of those with acute diarrhea. Furthermore, when the EAggEC were subdivided into aggregative adherence (AA) gene probe positive (18/56; 32%) and negative (20/56; 36%), both subgroups were still significantly different from controls [6/42 (14%) and 7/42 (17%), respectively; both p's < 0.05].(ABSTRACT TRUNCATED AT 250 WORDS)