Insulin resistance is a key defect associated with obesity, type 2 diabetes and other metabolic diseases. While a number of factors have been suggested to cause defects in insulin action, there is a very strong association between inappropriate lipid deposition in insulin target tissues and the development of insulin resistance. In recent times, a large number of studies have reported changes in markers of mitochondrial metabolism in insulin-resistant individuals, leading to the theory that defects in mitochondrial substrate oxidation are responsible for the buildup of lipid intermediates and the development of insulin resistance. The primary support for the mitochondrial theory of insulin resistance comes from studies in skeletal muscle; however, there is recent evidence in murine models that mitochondrial dysfunction in oocytes may also play a role. Oocytes from obese or insulin-resistant mice have been shown to exhibit abnormalities in many different mitochondrial parameters, including mitochondrial morphology and membrane potential. Here we review the findings regarding the link between mitochondrial dysfunction and insulin resistance, and propose that abnormalities in mitochondrial metabolism in oocytes may predispose to the development of obesity and insulin resistance and thus contribute to the inter-generational programming of metabolic disease.