We have previously reported on development of a simple PCR-based method to detect Plasmodium falciparum in which patient blood samples are lysed and then filtered onto paper. The present studies, conducted in Thailand, were designed to identify factors contributing to differences between results from microscopy and PCR. To analyze microscope-positive, PCR-negative results, we demonstrated that using the lysis/filtration sample preparation method, target DNA degradation is not a significant factor. Similarly, we showed that sensitivity of PCR among patient samples did not differ using the lysis centrifugation method or organically extracted DNA. We further demonstrated that 7/13 samples which were negative by PCR for P. falciparum were positive by PCR when P. vivax-specific primers were used. Microscope-negative, P. falciparum PCR-positive samples were analyzed in two ways: the true rate of false-positivity for PCR (2%) was established by analyzing 498 samples from patients living in areas without transmission. We further showed that when microscope-negative, PCR-positive samples were amplified using an independent P. falciparum-specific PCR target sequence, 42/47 were PCR-positive. We conclude that the accuracy and reduced limit of detection of microscopy are major confounders when comparing this method to PCR.