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Background: Preventive chemotherapy is the current global control strategy for schistosomiasis. The WHO target coverage rate is at least 75% for school-aged children. In the Philippines, the reported national coverage rate (43.5%) is far below the WHO target. This study examined the factors associated with non-compliance to mass drug administration., Methods: A cross-sectional survey was conducted in 2015 among 2189 adults in the province of Northern Samar, the Philippines using a structured face-to-face survey questionnaire., Results: The overall rate of non-compliance to mass drug administration (MDA) in the last treatment round was 27%. Females (aOR = 1.67, P = 0.033) were more likely to be non-compliant. Respondents who believed that schistosomiasis was acquired by open defecation and poor sanitation (aOR = 1.41, P = 0.015), and by drinking unclean water (aOR = 2.09, P = 0.001) were more likely to refuse treatment. Uncertainties on whether schistosomiasis can be treated (aOR = 2.39, P = 0.033), their fear of adverse reactions to praziquantel (aOR = 1.94, P = 0.021), misconceptions about alternative forms of treatment (aOR = 1.45, P = 0.037), and that praziquantel is used for purposes other than deworming (aOR = 2.15, P = 0.021) were all associated with a higher odd of non-compliance. In contrary, being a farmer (aOR = 0.62, P =0.038), participation in past MDA (aOR = 0.30, P < 0.001), informed about impending MDA (aOR = 0.08, P < 0.001), and having heard of schistosomiasis (aOR = 0.22, P = 0.045) were all significantly associated with reduced non-compliance., Conclusions: To improve drug compliance for schistosomiasis there is an urgent need for intensive health education campaigns before conducting MDA that would not only provide disease specific information, but also deal with prevailing misconceptions about transmission, prevention, treatment, and drug side-effects.