The aim of the study was to investigate allelic distribution of calcineurin gene (CNB; 5I/5D polymorphism) in athletes of cyclic sports (n = 673) and controls (n = 1073), and to find interrelation between genotypes and risk of left ventricular hypertrophy and physical performance of athletes. Genotyping was performed by restriction fragment length polymorphism. Echocardiography was performed by ultrasound scanner Aloka-3500. Physiological parameters were evaluated by spiroergometry using MetaMax 3B Gas Analyzer. The frequency of CNB D allele was significantly lo- wer in athletes than in controls (5.5 vs. 8.8 %; p = 0.0005), and decreased with the growth of skills. We found that CNB D allele was associated with increased left ventricular mass index and low values of physical performance (when maximal power production capacity and maximal oxygen consumption were measured). Thus, CNB gene 5I/5D polymorphism is associated with the risk of left ventricular hypertrophy and physical performance of athletes.