The number of people affected by metabolic diseases, such as type 2 diabetes is increasing worldwide. Metabolic diseases are complex multifactorial disorders caused by genetic and environmental factors, where the prenatal environment also seems to play a prominent role through establishment of an epigenetic memory. Accumulating evidence suggests that aging and lifestyle factors including diet and physical activity have long-lasting effects on the epigenome, which thereby might serve as a prognostic marker, and influence the risk of metabolic diseases later in life. These epigenetic alterations may also be passed on to further generations through transgenerational inheritance. Therefore, the discovery of epigenetic modifications as biomarkers may lead to future prevention and individualized treatment of metabolic diseases. Here, we review recent studies that provide links between epigenetics and development of metabolic diseases.