The aim of the study was to investigate allelic distribution of the mitochondrial transcription factor gene (TFAM) Ser12Thr polymorphism in athletes (n = 1537) and controls (n = 1113), and to find interrelation between genotypes and aerobic capacity in rowers (n = 90). Genotyping was performed by restriction fragment length polymorphism analysis. Aerobic capacity (maximal oxygen consumption (VO2max) and maximal power production capacity (Wmax)) was determined using an incremental test to exhaustion by rower ergometer. The frequency of TFAM 12Thr allele was significantly higher in endurance-oriented athletes (n = 588) than in controls (14.0% vs. 9.1%; p <0.0001), and increased with the growth of skills. Furthermore, TFAM 12Thr allele was associated with high values of aerobic performance (when Wmax and VO2max were measured). Thus, TFAM gene Ser12Thr polymorphism is associated with physical performance of athletes.