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BACKGROUND: Schistosomiasis is one of the neglected tropical diseases endemic to Mali. There has been insufficient investigation of the morbidity burden in highly endemic irrigated rice areas with the ongoing mass drug administration with praziquantel. In February 2005, a year after an initial mass drug administration in 2004, we performed the first cross-sectional survey of schistosomiasis in the Kokry-Bozo village in the Office du Niger rice irrigation region. In the fourteen years since this survey, there has been almost no research into schistosomiasis morbidity in Mali due to lack of funding. Therefore, the 2005 survey supplies near-baseline data for any future research into the treatment impacts in the area. METHODS: One hundred and ninety-four children aged 6-14 years from two schools were assessed for bladder pathology by ultrasound, and for anaemia and micro-haematuria by laboratory tests. Schistosoma eggs were examined microscopically in fresh stool and urine samples. Multivariate logistic regression analysis quantified the association of Schistosoma infections with anaemia, bladder pathology and micro-haematuria. Akaike’s information criterion was used to test the assumption of linear effects of infection intensity classes and used to compare across models. RESULTS: The overall prevalence of schistosomiasis in 189 school children was 97%; 17% (33/189) had a single infection (S. mansoni,13%, or S. haematobium, 4%) and 80% (156/189) were co-infected with S. mansoni and S. haematobium. The overall prevalence of S. mansoni with light infection was 27% (53/194), moderate infection was 24% (47/194) and heavy infection was 42% (81/194). Of the 194 of children investigated for S. haematobium 59% (114/194) had light infection and 26% (50/194) had heavy infection. No hookworm eggs were detected. The level of abnormal bladder pathology was 18% (35/189) with the highest found in 10-14 year old children. The prevalence of anaemia was 91% (172/189) and was twice as likely to be associated (OR 2.0, 95% CI 1.1-3.9) with S. mansoni infections than in children without infection. As infection intensity with S. mansoni increased the risk of anaemia (OR 2.0, 95% CI 1.1-3.9) also increased. As infection intensity with S. haematobium increased bladder pathology (OR 2.4, 95%CI 1.3-4.5), haematuria (OR 6.7, 95%CI 3.3-13.6) and micro-haematuria increased (OR 2.4, 95%CI 1.3-4.5). CONCLUSION: Our research contributes an important micro-geographical assessment of the heavy burden of schistosomiasis and associated morbidity in children who live in the rice irrigation regions. Our literature review found that there has been very limited research conducted on the impact of the treatment to control morbidity in the ON. Therefore, there is a need to do a comparable, but more extensive, study to identify any changes in morbidity and to indicate current requirements for the control programme. Our results from 2005 called for routine integration of iron supplementation, food fortification and diet diversification into the deworming program.