Chloroquine resistance in Plasmodium falciparum bears a striking similarity to the multi-drug resistance (MDR) phenotype of mammalian tumour cells which is mediated by P-glycoprotein. P. falciparum has two mdr-like genes (pfmdr 1 and pfmdr 2) and pfmdr 1 has been linked to the chloroquine resistance phenotype. We show that pfmdr 1 encodes a protein of 160,000 Daltons that is expressed at higher levels in a chloroquine resistant cloned isolate. The pfmdr 2 gene is located on chromosome 14 and it is in equal copy number in chloroquine resistant and sensitive isolates. Therefore amplification of pfmdr 2 is not linked to chloroquine resistance. This is in contrast to the pfmdr 1 gene which has been shown to be amplified in some chloroquine resistant isolates.