The mitochondrial diseases or diseases of the oxidative phosphorylation system (OXPHOS) consist of a group of disorders originated by a deficient synthesis of ATP. OXPHOS is composed of proteins codified in the two genetic systems of the cell, the nuclear and the mitochondria genomes and, therefore, the mode of inheritance could be either mendelian or maternal. Due to the central role that mitochondria plays in the cellular physiology, these diseases are, nowadays a social and health problem of great importance, and, although individually they are clasified among the rare diseases, all together constitute a large variety of genetic disorders. Beside this, it is considered that the mitochondria are involved, directly or indirectly, in a large percentage of the human diseases. In this review we will be mainly focussed to describe, from a genetic point of view, the diseases caused by mitochondrial DNA damage, to show the special characteristics of the mitochondrial genetic system, the different methods that are necessary to utilize for their correct diagnoses, remarking the difficulties to study these pathologies, and the possible implication of the genetic variability of the genome in the development of these diseases. At the end, a brief mention to the diseases caused by nuclear defects will also be made.