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This study evaluated a school-based and a community-based scheme for diagnosis, treatment and follow-up of schistosomiasis mansoni among school-aged children in views of resolution CD49.R19 of the Pan American Health Organization toward the elimination of schistosomiasis as a public health problem in the Americas and subsequent commitments endorsed by the Brazilian government. The school-aged population from a representative municipality of the endemic area of Northeastern Brazil was randomly allocated to either school-based or community-based scheme. The two schemes were compared with regard to coverage of diagnosis by the Kato-Katz method (KK) at baseline, treatment of the positives for Schistosoma mansoni with praziquantel, treatment of the positives for soil-transmitted helminthes (STH) with mebendazole, as well as follow-up of treatment efficacy and reinfection assessed respectively at four and 12 months after treatment. Nutritional status of the positives for S. mansoni was assessed at baseline and re-assessed at 12 months after treatment. Coverage of diagnosis and treatment was satisfactory (>75%) in both schemes. Diagnosis coverage at baseline and at 12 months was significantly higher in the community scheme, whereas treatment coverage did not differ significantly between the two schemes either at baseline or at 12 months. The number of children covered per day was significantly higher in the schools than in the community at baseline but not at follow-up, when daily coverage was higher in the community. With regard to S. mansoni, overall treatment efficacy rate at four months was 90.8%, and reinfection rate at 12 months was 21.6%. For STH, overall treatment efficacy was 45.4% and reinfection, 32.8%. The nutritional status of the positives for S. mansoni at baseline did not change significantly at 12 months post-treatment. Actions targeted at this particularly vulnerable high-risk group should combine school-based and community-based interventions as well as preventive measures to reduce transmission.