This report examines the relationship between two different diagnostic tests used in nationally-representative household surveys to measure malaria parasitemia prevalence: Rapid Diagnostic Tests (RDTs) and microscopy. Prevalence estimates from 22 surveys containing both microscopy and RDT results were compared using tests of agreement, and factors that could be influencing discordance between the two tests were identified. Although prevalence estimates from the two tests were highly correlated, RDT prevalence estimates were higher than microscopy prevalence estimates in 19 of 22 surveys examined. Given the lack of a gold standard diagnostic test for malaria that is practical for use in national survey settings, discrepancies in prevalence estimates generated from microscopy testing and from RDT testing are difficult to reconcile. Although results of these tests could be useful in identification of high-risk populations for targeting of interventions, assessments of impact based on changes in malaria prevalence measured with these tests are more problematic. Development of an algorithm for program managers to use to best estimate national prevalence given the available diagnostic data would be useful for the future.