Heteroduplex tracking assays (HTAs) of Plasmodium falciparum merozoite surface protein 1 block-2 were used to assess complexity of infection and treatment efficacy in a trial of three antimalarial treatments in 141 Malawian pregnant women. An elevated complexity of infection (COI) was associated with anemia, parasite burden, and human immunodeficiency virus infection but was not associated with age or gravidity. Comparisons of HTA patterns before and after treatment allowed the classification of 20 of 30 (66%) recurrent episodes as either definite treatment failures or reinfections. An elevated COI was strongly associated with treatment failure (P ؍ 0.003). An algorithm was developed to assign a probability of failure for the 10 indeterminate participants, some of whose infections shared a single variant of high prevalence (>10%). By summing these probabilities, treatment efficacy was estimated.More than 500 million people suffer from Plasmodium falciparum malaria each year. The majority of all malaria infections occur in sub-Saharan Africa, where there is often intense year-round exposure to infected mosquitoes (20). Probably as a result of frequent infectious bites, malaria infections in subSaharan Africa are usually polyclonal (2, 3, 13). Individual patients have been infected with as many as 14 genetically distinct parasite subpopulations or "variants" (3, 6, 11). The complexity of infection (COI), which is the number of variants in an individual host, has been measured by a variety of molecular methods. These methods include nested PCR, restriction fragment length polymorphism, microsatellite analysis, pyrosequencing, and PCR with a fluorescence primer followed by capillary electrophoresis (7,14,19,21).Using these molecular tools, a higher COI has been associated with symptomatic malaria manifestation in pregnant women (3). In a recent study, the risk of treatment failure in children was positively correlated with the COI (13).The current World Health Organization protocol recommends that all clinical efficacy studies with more than 14 days of follow-up use PCR-based methods to determine whether recurrent infection is due to drug failure (recrudescence) or a newly acquired infection (reinfection) (25). The inherent limitations of conventional nested PCR genotyping, such as sensitivity only to size differences, and different interpretations of the PCR comparisons can both have a dramatic impact on the treatment failure rate (18). Therefore, more definitive methods are needed.We have previously used the heteroduplex tracking assay (HTA) in an area of low malaria transmission to characterize the COI in Southeast Asia (15, 26). In the HTA, radiolabeled P. falciparum merozoite surface protein 1 (PfMSP1) probe is annealed to amplicons from a patient whose PfMSP1 block-2 region has undergone a single round of PCR amplification. Double-stranded complexes are formed between the probe and host amplicon(s); these complexes, termed heteroduplexes, migrate on a nondenaturing gel at various speeds based on the compleme...