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Objective: To conduct a nationwide integrated neglected tropical disease (NTD) prevalence survey to define the need for public health interventions using an innovative mapping protocol., Methods: Two villages were selected in every peripheral health unit in endemic districts: 29 districts for schistosomiasis and STH, 15 of them for trachoma. In each village, 15 children aged 6-9 years at a randomly selected school were tested. An additional convenience sample of 35 children aged 1-5 years underwent an eye examination for trachoma. This integrated mapping was followed by a 20-cluster trachoma survey in each district that surpassed the WHO-defined threshold of 10% prevalence of trachomatous inflammation-follicular (TF)., Results: A total of 1096 villages were surveyed in <6 weeks. The district prevalence of schistosomiasis ranged from 2 to 49% and of STH from 5 to 70%, with prevalence at the village level ranging from 0 to 100% for both diseases. Two districts passed the threshold of 10% for active trachoma, but the cluster survey indicated this was because of misclassification bias and that the real prevalence was <1%., Conclusion: Results of this mapping were used by the MoH and partners to plan integrated mass drug administration (MDA). Mass drug administration for trachoma was not implemented as no district passed the threshold requiring public health intervention., (© 2012 Blackwell Publishing Ltd.)