Resistance to the amino alcohol quinine has been associated with polymorphisms in pfnhe, a sodium hydrogen exchanger. We investigated the role of this gene in quinine resistance in vitro in isolates from Kenya. We analyzed pfnhe whole-gene polymorphisms, using capillary sequencing, and pfcrt at codon 76 (pfcrt-76) and pfmdr1 at codon 86 (pfmdr1-86), using PCR-enzyme restriction methodology, in 29 isolates from Kilifi, Kenya, for association with the in vitro activities of quinine and 2 amino alcohols, mefloquine and halofantrine. In vitro activity was assessed as the drug concentration that inhibits 50% of parasite growth (IC 50 ). The median IC 50 s of quinine, halofantrine, and mefloquine were 92, 22, and 18 nM, respectively. The presence of 2 DNNND repeats in microsatellite ms4760 of pfnhe was associated with reduced susceptibility to quinine (60 versus 227 nM for 1 and 2 repeats, respectively; P < 0.05), while 3 repeats were associated with restoration of susceptibility. The decrease in susceptibility conferred by the 2 DNNND repeats was more pronounced in parasites harboring the pfmdr1-86 mutation. No association was found between susceptibility to quinine and the pfcrt-76 mutation or between susceptibility to mefloquine or halofantrine and the pfnhe gene and the pfcrt-76 and pfmdr1-86 mutations. Using previously published data on the in vitro activities of chloroquine, lumefantrine, piperaquine, and dihydroartemisinin, we investigated the association of their activities with pfnhe polymorphism. With the exception of a modulation of the activity of lumefantrine by a mutation at position 1437, pfnhe did not modulate their activities. Two DNNND repeats combined with the pfmdr1-86 mutation could be used as an indicator of reduced susceptibility to quinine.The amino alcohol quinine (QN) remains one of the important drugs against malaria. It is the drug of choice for the treatment of severe malaria, and in most African countries, including Kenya, where artemisinin-based combinations (lumefantrine-artemether, amodiaquine-artesunate) are now first-line treatments, 7-day quinine monotherapy has become the second-line treatment for uncomplicated malaria (44). However, there is evidence of selection and spread of QN-resistant parasites or those with reduced susceptibility to 8,30,34). This observation led to the investigation of artesunate (an artemisinin derivative) as an alternative to QN for the treatment of severe malaria (14). However, this option could now be compromised by the emergence of artemisinin resistance (9).Several studies have been dedicated to understanding the mechanisms of quinine resistance. Polymorphisms in pfmdr, a gene associated with chloroquine (CQ) resistance, modulate QN susceptibility (27,33,36). A mutation of the CQ resistance gene pfcrt at codon 76 (pfcrt-76) has been associated with reduced susceptibility to QN in vitro, although transfection studies have shown conflicting results (16,37). A seminal study on the association of polymorphisms in pfnhe, a sodium hydrogen exchanger gene, a...