cThe ongoing development of new antimalarial drugs and the increasing use of controlled human malaria infection (CHMI) studies to investigate their activity in early-stage clinical trials require the development of methods to analyze their pharmacodynamic effect. This is especially so for studies where quantitative PCR (qPCR) is becoming the preferred method for assessing parasite clearance as the study endpoint. We report the development and validation of an analytic approach for qPCR-determined parasite clearance data. First, in a clinical trial with the licensed antimalarial combination sulfadoxine-pyrimethamine (S/P), qPCR data were collected from 12 subjects and used to determine qPCR replicate variability and to identify outliers. Then, an iterative analytic approach based on modeling the log-linear decay of parasitemia following drug treatment was developed to determine the parasite reduction ratio (PRR) and parasite clearance half-life, both measures of parasite clearance. This analytic approach was then validated with data from 8 subjects enrolled in a second study with the licensed antimalarial drug mefloquine. By this method, the PRR and parasite clearance half-lives for S/P and Mefloquine were determined to be 38,878 (95% confidence interval A critical determinant of the success of antimalarial chemotherapy is the speed of clearance of parasites from the blood of infected individuals. Indeed, this pharmacodynamic relationship represents one of the few clinically validated examples in antimicrobial chemotherapy. For example, the superiority of artemisinin antimalarials over comparator drugs, such as quinine, in terms of clinical endpoints can be attributed to the more rapid clearance of parasites from the blood following artemisinin combination chemotherapy (ACT) (1). Indeed, the increasing number of reports from the Greater Mekong Delta of slower clearance of Plasmodium falciparum from the blood following ACT forebodes worsening clinical outcomes (2-5).Quantification of parasitemia has generally relied on counting parasites on blood films. Advantages of this methodology include the ease of collection from finger prick, the low cost of consumables, and well-standardized methods. Additional useful information can be obtained from blood films, including infection with mixed parasite species, the presence of different life cycle stages, and the presence of malaria pigment in white cells. Disadvantages include the need for skilled microscopists who regularly undertake Quality Assurance Programs, the inferior sensitivity of microscopy compared to molecular techniques, and the time-consuming nature of reading multiple slides in the context of an ongoing clinical trial. Although quantitation of biomarkers of parasite biomass, such as histidine-rich protein 2, has some utility in measuring parasite biomass (6), it is not well suited for serial estimation of changes in parasite density in the context of drug treatment due to the kinetics of clearance of circulating parasite antigen differing from that of paras...