Background In Uganda, the current national health sector strategic and investment plan underscores schistosomiasis as one of the diseases targeted for elimination by the year 2015. However, uptake of treatment among school children is unknown but suspected to be low. We estimated the uptake and predictors of preventive treatment with praziquantel. Methods In a cross sectional study carried out in Jinja district of Uganda, a random sample of 1,010 children in 12 primary schools was questioned about their uptake of praziquantel, knowledge and perceptions about schistosomiasis, support for taking preventive treatment and the dangers of taking praziquantel. The prevalence and mean intensity of infection with Schistosoma mansoni were determined. Results Self reported uptake of praziquantel at last mass treatment was 28.2% (95% confidence interval (CI): 22.9%–33.6%). Overall prevalence and mean intensity of S. mansoni infection was 35% (95% CI: 25.4%–37.9%) and 116.1 eggs per gram (epg) of stool (95% CI: 98.3–137.1) respectively. Uptake of praziquantel was more likely if a child was from a school with high prevalence of infection, had knowledge about schistosomiasis transmission and prevention, and reported teachers’ support to take praziquantel. Of the 285 children who took praziquantel, 142 (49.8%) developed side effects. Of the 725 children who did not take the drug, 522 (72.0%) reported fear of side effects as a major reason for non-uptake. Conclusions Uptake of praziquantel in this population is very low. Fear of side effects of praziquantel, lack of knowledge about schistosomiasis transmission and prevention and lack of teacher support are some of the major factors associated with low uptake.
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