We replicated and extended this work by examining polymorphisms in these genes and in vitro resistance to eight drugs in parasites collected from the Thailand-Burma border. To minimize problems of multiple testing, we used a two-phase study design, while to minimize problems caused by population structure, we analyzed parasite isolates collected from a single clinic. We first examined associations between genotype and drug response in 108 unique single-clone parasite isolates. We found strong associations between single nucleotide polymorphisms in pfmdr and mefloquine (MFQ), artesunate (AS), and lumefantrine (LUM) response. We also observed associations between an ABC transporter (G7) and response to QN and AS and between another ABC transporter (G49) and response to dihydro-artemisinin (DHA). We reexamined significant associations in an independent sample of 199 unique single-clone infections from the same location. The significant associations with pfmdr-1042 detected in the first survey remained. However, with the exception of the G7-artesunate association, all other associations observed with the nine new candidate transporters disappeared. We also examined linkage disequilibrium (LD) between markers and phenotypic correlations between drug responses. We found minimal LD between genes. Furthermore, we found no correlation between chloroquine and quinine responses, although we did find expected strong correlations between MFQ, QN, AS, DHA, and LUM. To conclude, we found no evidence for an association between 8/9 candidate genes and response to eight different antimalarial drugs. However, the consistent association observed between a 3-bp indel in G7 and AS response merits further investigation.Transporter loci are attractive candidates for antimalarial drug resistance genes. Two of four known drug resistance loci in Plasmodium falciparum are transporters, and transporters play major roles in drug resistance in both bacteria and cancer cells (1, 6, 13). A previous study (14) located 49 genes encoding transporters in the P. falciparum genome and sequenced these genes in a panel of 97 isolates from worldwide locations. Polymorphisms in 11/49 genes showed significant association with in vitro drug resistance to chloroquine (CQ) and/or quinine (QN). Two of these genes, pfcrt and pfmdr, are already known to play a role in resistance (9,12,26,28), while the remaining nine candidates are new. Of these nine candidates, six were associated with either a CQ response or a QN response in a southeast Asian population sample. There was also strong linkage disequilibrium (LD) between loci on different chromosomes, consistent with coselection or epistasis (8), and strong correlations between 50% inhibitory concentrations (IC 50 ) with CQ and QN, suggesting that common genes may underlie resistance to both drugs.While these results are exciting, some caution is needed in interpreting such candidate gene studies. There are two particular problems. First, when multiple tests are carried out, some significant results may occur by...