Atovaquone-d is intended for use as an internal standard for the quantification of atovaquone by GC- or LC-MS. Atovaquone is a broad-spectrum antiprotozoal agent that is active against Plasmodium, Toxoplasma, and Babesia, among other protozoa. It inhibits complex III activity on dihydroorotate in isolated P. falciparum and P. yoelii mitochondria more potently than in rat liver mitochondria (ECs = 0.95, 0.94, and 510 nM, respectively) and depolarizes the mitochondrial membrane in P. yoelii-infected mouse erythrocytes (EC = 260 nM). Atovaquone also inhibits transport mediated by human breast cancer resistance protein (BCRP) and P-glycoprotein in membrane vesicles (ICs = 0.23 and 6.8 μM, respectively). It inhibits the growth of T. gondii in MRC-5 human lung fibroblasts in vitro (IC = ~64 nM) and increases mean survival of T. gondii-infected mice from 5.5 to 21.2 days when administered at a dose of 100 mg/kg per day. Formulations containing atovaquone have been used in the treatment of Pneumocystis pneumonia and toxoplasmosis as well as in combination with proguanil in the treatment of malaria and babesiosis.