Zidovudine (azidothymidine [AZT]) inhibits human immunodeficiency virus replication and reduces the severity of acquired immunodeficiency syndrome. A limiting side effect of AZT is a mitochondrial cardiac and skeletal myopathy in which the pharmacologically active derivative of AZT (AZT triphosphate) plays a critical role. The present study determined biochemical mechanisms of AZT-induced mitochondrial toxicity and identified AZT triphosphate as an inhibitor of DNA polymerase-γ in vitro. Inhibition kinetics were defined using purified bovine cardiac mitochondrial DNA polymerase-γ and AZT triphosphate in vitro. The Km for deoxythymidine triphosphate was 0.8±0.3 μmol/L. AZT triphosphate incubation with DNA polymerase-γ in vitro resulted in mixed kinetics with a competitive Ki of 1.8±0.2 μmol/L and a noncompetitive Ki' of 6.8±1.7 μmol/L. These Ki and Ki' values were strikingly higher than values for retroviral reverse transcriptase but lower than values for other cellular DNA polymerases. These data support previous molecular and morphological findings in clinical AZT mitochondrial myopathy and in models of AZT myopathy in vivo. Biochemical findings suggest that inhibition of mitochondrial DNA polymerase-γ may be integral to the pathogenesis of AZT-induced myopathy.