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Currently, a 30-cluster survey to monitor drug coverage after mass drug administration for neglected tropical diseases is the most common methodology used by control programs. We investigated alternative survey methodologies that could potentially provide an estimation of drug coverage. Three alternative survey methods (market, village chief, and religious leader) were conducted and compared to the 30-cluster method in Malawi, Mali, and Uganda. In Malawi, drug coverage for the 30-cluster, market, village chief, and religious leader methods were 66.8% (95% CI 60.3-73.4), 74.3%, 76.3%, and 77.8%, respectively. In Mali, results for round 1 were 62.6% (95% CI 54.4-70.7), 56.1%, 74.8%, and 83.2%, and 57.2% (95% CI 49.0-65.4), 54.5%, 72.2%, and 73.3%, respectively, for round 2. Uganda survey results were 65.7% (59.4-72.0), 43.7%, 67.2%, and 77.6% respectively. Further research is needed to test different coverage survey methodologies to determine which survey methods are the most scientifically rigorous and resource efficient