Chloroquine (CQ) is commonly used for treatment of malaria; however, its mode of action and the mechanism of resistance are still not fully understood. Better knowledge of CQ's mode of action may make it possible to identify new drugs that target similar pathways or to reverse existing resistant phenotypes. CQ has been shown to interact in both mammalian cells and Plasmodium spp. with a number of different pathways, including changes in vacuolar (or lysosomal) pH (9, 22, 39, 56), binding to DNA and RNA (3, 11, 41, 53), binding to heme and β-hematin in Plasmodium falciparum (1, 55; reviewed in reference 20). In the case of P. falciparum, CQ was an effective drug whose efficacy has been severely compromised by the emergence of drug-resistant parasites (8, 20). To analyze the mechanism of CQ action, we used transcriptional profiling in a model eukaryotic system, Saccharomyces cerevisiae. Differential transcriptional profiling using microarray analysis is based on detecting differences in expression of mRNAs in cells treated under different conditions. No information other than the genomic sequence and the open reading frame (ORF) predictions is necessary to assay mRNA expression. Such whole-genome analysis allows the determination of expression profiles without preselection of genes. For the experiments described here, we used the Affymetrix Yeast Chip YE6100, which is based on the oligonucleotide array method. We published the adaptation of this system to the wild-type S. cerevisiae strain YPH499 and derivatives previously (38). From this transcriptional profile analysis, we identified a number of genes whose products are involved in metal acquisition and metabolism that have increased mRNA levels during challenge with CQ. Increased expression of genes involved in iron (Fe) availability suggested that CQ toxicity might, in part, result from interference with iron uptake or metabolism. Although CQ has been demonstrated to disrupt iron trafficking in several cell types, including pathogenic yeasts (9, 22, 39), the observation of altered expression of iron metabolism genes in S. cerevisiae was surprising. In all these cases, CQ disrupts iron trafficking by increasing pH in lysosomes and preventing the release of iron from the carrier proteins. No iron carrier protein system has been identified in S. cerevisiae, and thus, this mechanism of CQ action is very unlikely in S. cerevisiae. Therefore, we initiated a more thorough investigation of genes involved in metal transport and availability, with particular interest in those involved with iron transport. In this study, we investigated the role of CQ in iron trafficking using a variety of approaches involving pharmacological, genetic, and biochemical techniques. One of the advantages of the S. cerevisiae system is the availability not only of the whole genome sequence but also of mutants deficient in specific genes or combinations of genes, thus allowing genetic dissection of pathways. For these experiments, we utilized yeast lacking the major iron uptake pathways (Fet3 and Fet4) as well as yeast deficient in SIT1, the major iron siderophore transporter that is induced under CQ pressure.