The etiology of bloody diarrhea was investigated in a cohort of 75 children followed longitudinally from birth during the first two years of life in a rural Village of Central Mexico. Of a total of 636 episodes of diarrhea, 71 (11%) showed presence of blood. A single associated pathogen was isolated in 59 (83%) of 71 children; 35% showed the presence of enteroaggregative E. coli (EAEC), 11% of E. coli producing Shiga-like toxins (SLT) I and/or II; 13% of Shigella, 7% of Campylobacterjejuni or enterotoxigenic E. coli (ETEC) and 4% enteropathogenic E. coli (EPEC), enteroinvasive E. coli (EIEC), Salmonella, Giardia lamblia or Hymenolepis nana. Mixed cultures were found in 16% of cases during the first year and in 18% during the second. These were mainly combinations of C. jejuni, with ETEC or EAEC. In 78% of children with bloody diarrhea the episode was single event during the first two years of life, lasting on average seven days. Epidemiologically, the incidence of bloody diarrhea rose steadily during the first two years of life, with a significant decrease after the tenth month. Prevalence was affected by seasonality in all pathogens, except for EAEC that had an endemic frequency. In the case of Shigella and SLT-producing E. coli clustering of cases and isolation of serologically identical strains indicated that infections were the result of common source outbreaks.