Abstract. Mutations in the Pfmdr1 gene are reported to be associated with chloroquine resistance in some Plasmodium falciparum isolates. A polymerase chain reaction/restriction fragment length polymorphism method was used for the detection of Pfmdr1 mutations in chloroquine-resistant field isolates of P. falciparum collected in Irian Jaya. The frequency of Pfmdr1 mutations was significantly higher in chloroquine-resistant P. falciparum parasites than background frequencies observed in the same location. The 7G8 mutation was identified in some parasites although always in a mixed genotype status. Chloroquine-resistant P. falciparum specimens were characterized using the World Health Organization 28-day criteria, supplemented by demonstrating adequate chloroquine absorption and genetic analysis.Resistance of Plasmodium falciparum to chloroquine (CQ) and other antimalarial drugs is a widespread phenomenon that challenges current control efforts. Since early reports in the late 1950s, CQ resistance has been identified in most regions of the world where malaria is endemic. This problem has been investigated in several islands of the Indonesian archipelago such as Lombok, 1 Java, 2 and Irian Jaya, [3][4][5] where the first Indonesian case of CQ-resistant P. falciparum was described. 6 To understand the mechanism of CQ resistance in malaria parasites, a search for the responsible gene(s) has been launched. In 1989 two P. falciparum genes homologous to the mammalian multiple drug resistance (MDR) gene were identified, mapped to chromosome V, 7 and named Pfmdr1 and Pfmdr2. 8 This discovery, coupled with the fact that the calcium channel blocker verapamil reverses CQ resistance, 9 gave support to the theory that a mechanism similar to multiple drug resistance in mammalian tumor cells, in which over expression and amplification of the MDR gene confers drug resistance to tumor cells via an efflux mechanism, operates in P. falciparum. The product of the Pfmdr1 gene, Pglycoprotein homolog 1 (Pgh1) has been localized to the membrane of the digestive vacuole of mature blood stage parasites. 10 This model predicted that the Pfmdr1 gene would be amplified and/or over expressed in CQ-resistant isolates but several studies obtained mixed results. [11][12][13][14][15] Considerable controversy has been generated by conflicting reports that tested a second model: that mutations in the Pfmdr1 gene confer CQ resistance. DNA sequencing of the Pfmdr1 gene from reference strains and field isolates has revealed several point mutations that correlated with CQ resistance. 16 These mutations were classed into two genotypes: the K1 genotype, resulting in an asparagine (Asn) to tyrosine (Tyr) change at position 86 and the 7G8 genotype, with four point mutations resulting in amino acid substitutions at positions 184, 1034, 1042, and 1246. Shortly after a rapid polymerase chain reaction (PCR) and restriction digest method for the detection of these two genotypes in field isolates was developed;17 field studies applied this technique and confirmed ...