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We report a simple method for the polymerase chain reaction (PCR) amplification of whole blood samples collected on filter paper. The blood spot was used directly in the PCR after treatment with methanol. We evaluated this assay using clinical samples collected from subjects in a Plasmodium falciparum vaccine trial and from samples collected during a hospital-based study in Thailand. Specimens prepared from heparinized blood samples were successfully amplified following pretreatment with heparinase. Sensitivity was 100% when compared with thick blood film results in the vaccine trial (range = 4–60 parasites/µl, median = 8/µl) and 94.6% (range = 3–133,988 parasites/µl, median = 616/µl) in the hospital study.