To determine the relative efficacy of metrifonate and praziquantel in controlling urinary tract morbidity due to Schistosoma haematobium infection, a random allocation treatment trial was performed among 1,813 school age S. haematobium-infected children from the Msambweni area of Coast Province, Kenya. Following baseline examination for infection, hematuria, proteinuria, and ultrasonographic urinary tract abnormalities, oral treatment with either metrifonate (10 mg/kg, repeated at 4 month intervals) or praziquantel (1 dose of 40 mg/kg) was given to infected subjects. Prevalence of morbidity was reassessed 12 months later for each treatment group. Results indicated equivalent patient improvement in response to either regimen: prevalence of hematiuria fell from 75% to 17% after either praziquantel or metrifonate therapy. Similarly, prevalence of proteinuria was significantly reduced from 73% to 29% (metrifonate) or 27% (praziquantel) after therapy. Metrifonate and praziquantel caused similar reductions in bladder granulomata and bladder thickening; however, no reduction in hydronephrosis was noted with either drug. Analysis of outcomes in population subgroups defined by age, sex, pretreatment intensity of infection, or severity of pretreatment morbidity showed no consistent advantage for either drug. In this endemic area, both agents provide effective control of morbidity due to urinary schistosomiasis.