At present, approaches to studying mitochondrial functions in malarial parasites are quite limited because of the technical difficulties in isolating functional mitochondria in sufficient quantity and purity. We have developed a flow cytometric assay as an alternate means to study mitochondrial functions in intact erythrocytes infected with Plasmodium yoelii, a rodent malaria parasite. By using a very low concentration (2 nM) of a lipophilic cationic fluorescent probe, 3,3dihexyloxa-carbocyanine iodide, we were able to measure mitochondrial membrane potential(⌬⌿ m ) in live intact parasitized erythrocytes through flow cytometry. The accumulation of the probe into parasite mitochondria was dependent on the presence of a membrane potential since inclusion of carbonyl cyanide m-chlorophenylhydrazone, a protonophore, dissipated the membrane potential and abolished the probe accumulation. We tested the effect of standard mitochondrial inhibitors such as myxothiazole, antimycin, cyanide and rotenone. All of them except rotenone collapsed the ⌬⌿ m and inhibited respiration. The assay was validated by comparing the EC 50 of these compounds for inhibiting ⌬⌿ m and respiration. This assay was used to investigate the effect of various antimalarial drugs such as chloroquine, tetracycline and a broad spectrum antiparasitic drug atovaquone. We observed that only atovaquone collapsed ⌬⌿ m and inhibited parasite respiration within minutes after drug treatment. Furthermore, atovaquone had no effect on mammalian ⌬⌿ m . This suggests that atovaquone, shown to inhibit mitochondrial electron transport, also depolarizes malarial mitochondria with consequent cellular damage and death.Plasmodium spp. are obligate intracellular parasites, spending a major portion of their life cycle within erythrocytes and converting these relatively inactive cells into metabolically thriving active hosts. At present, our knowledge of mechanisms by which the parasite accomplishes these changes is limited, as is our understanding of metabolic processes associated with parasitism. It is generally believed that glycolysis is the main source of ATP in erythrocytic stages of malarial parasites with little or no contribution by mitochondria to the cellular ATP pool (1, 2). A lack of tricarboxylic acid cycle enzymes (3-6) and an acristate mitochondrial morphology has led to the suggestion that mitochondria in malaria parasite act mainly to serve as an electron disposal sink for dihydroorotate dehydrogenase, a critical enzyme in pyrimidine biosynthesis (7-9). It is well established through studies in other systems that, in addition to oxidative phosphorylation, mitochondria are also central to many other physiological activities such as the metabolism of molecules such as amino acids, lipids, and heme, as well as intracellular Ca 2ϩ homeostasis (10). These functions are achieved by the action of gene products encoded by both mitochondrial and nuclear genomes. Because most of the mitochondrial proteins are encoded by the nuclear genome and imported into mitochon...