In Bolivia, few data are available to guide empiric therapy for bloody diarrhea. A study was conducted between December 1994 and April 1995 to identify organisms causing bloody diarrhea in Bolivian children. Rectal swabs from children <5 years old with bloody diarrhea were examined for Salmonella, Shigella, and Campylobacter organisms; fecal specimens were examined for Entamoeba histolytica. A bacterial pathogen was identified in specimens from 55 patients (41%). Shigella organisms were found in 39 specimens (29%); 37 isolates (95%) were resistant to ampicillin, 35 (90%) to trimethoprim-sulfamethoxazole, and 24 (62%) to chloramphenicol, but all were susceptible to nalidixic acid. Only 1 of 133 stool specimens contained E. histolytica trophozoites. Multidrug-resistant Shigella species are a frequent cause of bloody diarrhea in Bolivian children; E. histolytica is uncommon. Clinical predictors described in this study may help identify patients most likely to have Shigella infection. Laboratory surveillance is essential to monitor antimicrobial resistance and guide empiric treatment.