Chloroquine has been widely used for malaria treatment and prophylaxis for several decades, but its usefulness has now declined with the emergence of chloroquine resistance. Recent studies showed that the K76T mutation in the PfCRT protein, initially associated to chloroquine-resistant parasites, is sometimes also present in susceptible parasites, suggesting that other factors control the expression of the resistance phenotype. Here, we sought new mutations in the Pfcrt gene and used real-time PCR to investigate variations in the expression level of this gene with respect to the in vitro response to chloroquine. About 40 Cambodian isolates of Plasmodium falciparum were selected on the basis of their response to chloroquine in vitro. The Pfcrt gene was characterised by amplifying and sequencing the full-length cDNA. Twelve point mutations--M74I, N75D/E, K76T, A144F, L148I, I194T, A220S, Q271E, N326S, T333S, I356T and R371I--were detected. Mutations identified at positions 144, 148, 194 and 333 had never been described before. These mutations define six distinct haplotypes, distributed heterogeneously throughout Cambodia. Only the mutations at positions 74-76, 220 and 271 were significantly associated with the in vitro response to chloroquine. Three major haplotypes--MNK/A/Q, IDT/S/E and IET/S/E--accounted for all the isolates examined. The MNK/A/Q haplotype corresponded to susceptible isolates whereas parasites with the IDT/S/E haplotype displayed an intermediate response to chloroquine and those with the IET/S/E haplotype displayed the highest IC50 values. Phylogenic analysis suggested that the IDT and IET haplotypes (positions 74-76) arose independently from the wild-type MNK sequence. We found that the expression level of Pfcrt, evaluated by real-time PCR, had no effect on the response of the parasite to the drug in vitro. Similarly, in a CQ-resistant strain short-term cultured in the presence of CQ, no change was observed in the level of transcripts. These results are discussed in light of recent finding suggesting the possible involvement of other transporters in CQ-resistance.