In addition to external factors, such as exercise, food and the environment, genetic predisposition makes great contribution to the development of metabolic disorders and cardiovascular disease. This review is aimed to examine the genetic basis of complex metabolic disorders conventionally described as "metabolic syndrome" (MetS), with the special focus on currently known mutations in the nuclear and mitochondrial genomes, which are associated with both the individual components of MetS and combinations thereof, and also on the studies of the relationship of MetS phenotype as a binary trait. The defects in the mitochondrial genome should be considered as one of the possible genetic reasons leading to MetS. It is known that mitochondrial dysfunction is closely associated with metabolic disorders, as mitochondria are the center of energy metabolism. Consequently, the changes in mitochondrial genes and their functions affect regulation of metabolism. Until now, the role of mitochondrial DNA damage in the development of cardiovascular diseases, age-related and metabolic disorders is still poorly understood. The results of performed studies would help assessing the role of mitochondrial DNA mutations in susceptibility to metabolic syndrome and related metabolic diseases.