Viral infections frequently alter mitochondrial function with suppression or induction of apoptosis and enhanced generation of reactive oxygen species. The mechanisms of these effects are varied, and mitochondria are affected by both direct interactions with viral proteins and by secondary effects of viral-activated signaling cascades. This chapter describes methods used in our laboratory to assess the effects of the hepatitis C virus core protein on mitochondrial ROS production, electron transport, and Ca2+ uptake. These include measurements of the effects of in vitro incubation of liver mitochondria with purified core protein and assessment of the function of mitochondria in cells and tissues expressing core and other viral proteins. These methods are generally applicable to the study of viral-mitochondrial interactions.