Energy efficiency is one of the fundamental athletic performance-affecting features of the cell and the organism as a whole. Mitochondrial DNA (mtDNA) variants and haplogroups have been linked to the successful practice of various sports, but despite numerous studies, understanding of the correlation is far from being comprehensive. In this study, the mtDNA sequence and copy number were determined for 99 outstanding Polish male athletes performing in power (n = 52) or endurance sports (n = 47) and 100 controls. The distribution of haplogroups, single nucleotide variant association, heteroplasmy, and mtDNA copy number were analyzed in the blood and saliva. We found no correlation between any haplogroup, single nucleotide variant, especially rare or non-synonymous ones, and athletic performance. Interestingly, heteroplasmy was less frequent in the study group, especially in endurance athletes. We observed a lower mtDNA copy number in both power and endurance athletes compared to controls. This could result from an inactivity of compensatory mechanisms activated by disadvantageous variants present in the general population and indicates a favorable genetic makeup of the athletes. The results emphasize a need for a more comprehensive analysis of the involvement of the mitochondrial genome in physical performance, combining nucleotide and copy number analysis in the context of nuclear gene variants.