The prevalence of a genetic polymorphism(s) at codon 268 in the cytochrome b gene, which is associated with failure of atovaquone-proguanil treatment, was analyzed in 227 Plasmodium falciparum parasites from western Kenya. The prevalence of the wild-type allele was 63%, and that of the Y268S (denoting a Y-to-S change at position 268) mutant allele was 2%. There were no pure Y268C or Y268N mutant alleles, only mixtures of a mutant allele(s) with the wild type. There was a correlation between parasite 50% inhibitory concentration (IC 50 ) and parasite genetic polymorphism; mutant alleles had higher IC 50 s than the wild type.A tovaquone-proguanil (AP) is a fixed-dose combination antimalarial drug, mostly used for treatment and chemoprophylaxis of falciparum malaria for international travelers (1). Use of atovaquone alone leads to high rates of treatment recrudescence (2), which is attributed to mutations in the cytochrome b gene (pfcytb) (3). Plasmodium falciparum atovaquone-resistant isolates have been described following atovaquone or AP treatment failures (4-11) and in vitro drug susceptibility testing (5,8,10,12). In vitro and in vivo resistance to atovaquone has been associated with point mutations at codon 268 in pfcytb (5, 9, 10, 13). These mutations include Y268S (denoting the Y-to-S change at position 268), Y268N, and Y268C (5, 9, 11, 13, 14) and can induce a Ͼ1,000-fold increase in atovaquone 50% inhibitory concentration (IC 50 ) (13, 15). There are cases of AP treatment failure for travelers returning from Africa (4-6, 9-11, 16-19) and appearance of pfcytb mutations following AP treatment (4-6, 9-11, 14). However, treatment failure is not always associated with a known pfcytb mutation (17,18,20,21), indicating that other factors such as genetic polymorphisms in other genetic loci play a role in AP resistance.Kenya has a large number of international travelers and foreign residents who use AP for malaria prophylaxis. Additionally, AP is one of the second-line treatment options for uncomplicated malaria (22). In this study, a baseline epidemiological surveillance study was conducted to determine the prevalence of a genetic polymorphism(s) at codon 268 of pfcytb in Kenyan P. falciparum parasites. Field clinical isolates from an ongoing approved malaria epidemiological surveillance protocol (KEMRI SSC document 1330 and WRAIR document 1384), collected between 2008 and 2012 from three locations in Kenya (Kisumu, Kisii, and Kericho), were randomly selected for inclusion in the study. Kisumu is a lowland where malaria is endemic, with highly stable transmission, whereas Kisii and Kericho are highlands, with unstable transmission (23). Sample collection and preparation were performed as previously described (24). Genomic DNA from whole blood was extracted using a Qiagen DNA minikit (Qiagen, Valencia, CA) as recommended by the manufacturer. Clinical isolates were culture adapted before being subjected to the SYBR green I assay as previously described (25). A total of 227 (167 from Kisumu, 37 from Kisii, and 23 f...