Mitochondria play a key role in energy metabolism in many tissues, including skeletal muscle and liver. Inherent disorders of mitochondria such as DNA deletions cause major disruption of metabolism and can result in severe impairment or death. However, the occurrence of such disorders is extremely rare and cannot account for the majority of metabolic disease. Recently, mitochondrial dysfunction of a more subtle nature in skeletal muscle has been implicated in the pathology of chronic metabolic disease characterized by insulin resistance such as obesity, type 2 diabetes mellitus, and aging. This hypothesis has been substantiated by work from Shulman and colleagues, showing that reduced mitochondrial oxidative capacity underlies the accumulation of intramuscular fat causing insulin resistance with aging. However, recent work by Nair and coworkers has demonstrated that mitochondrial activity may actually be higher in persons exposed to high-calorie diet leading to obesity, suggesting that the accumulation of intramuscular fat and associated fatty acid metabolites may be directly responsible for the development of insulin resistance, independent of mitochondrial function. These inconsistent findings have promoted ongoing investigation into mitochondrial function to determine whether impaired function is a cause or consequence of metabolic disorders.