BACKGROUND: In sub-Saharan Africa, 112 million people are infected with Schistosoma haematobium, with the most intense infections in children 5-15 years old. METHODS: We describe a longitudinal epidemiological study that evaluates the relationship between S. haematobium infection and associated morbidity in children before and after the large-scale administration of praziquantel for schistosomiasis and albendazole for soil-transmitted helminths. RESULTS: At baseline, higher intensities of S. haematobium infection were observed in children with anemia and/or severe microhematuria, but there was no apparent association between the risk of undernutrition and intensity of S. haematobium infection. Significant reductions in the prevalence and intensity of S. haematobium infection 1 year after treatment were, however, observed. Children who benefited the most from anthelmintic treatment in terms of increased hemoglobin concentrations were those who had anemia at baseline and those with highly positive microhematuria scores at baseline. CONCLUSIONS: This study suggests that even a single round of mass chemotherapy can have a substantial impact on S. haematobium infection and its associated morbidity in children.