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Across 8101 individuals in 46 villages, the proportion of Plasmodium spp. multiple clone infections (0%-53.8%) did not reflect prevalence by quantitative polymerase chain reaction (qPCR; 1.9%-38.4%), except for P. vivax in Solomon Islands (P < .001). Thus this parameter was not informative to identify transmission foci. In contrast, prevalence by microscopy and qPCR correlated well.