BACKGROUND: There is little data available regarding the effects of male sex hormones on cardiac autonomic function. The aim of this study is to evaluate the association between hormones of male hypothalamo-pitiutary-gonadal axis and cardiac autonomic function by comparing heart rate variability (HRV) parameters of young male idiopathic hypogonadotropic hypogonadism patients with those of healthy controls. METHODS: The study consisted of 22 male idiopathic hypogonadotropic hypogonadism patients (mean age 20.8+/-1.2years) and the same number of age-matched healthy male controls (mean age 21.0+/-1.5years). A 24-hour Holter monitoring was performed to assess the time and frequency-domain parameters. The HRV parameters of patients and control groups were compared, and possible associations between levels of tested hormones and HRV parameters were evaluated. RESULTS: The standard deviation of all NN intervals (SDNN), standard deviation of the averages of NN intervals in all 5min segments (SDANN), power in low frequency range (LF, ms(2)) and power in high frequency range (HF, ms(2)) values of patients were significantly lower compared to those of controls (147.47+/-56.16 vs. 193.63+/-40.89; 138.31+/-57.64 vs. 190.15+/-43.94; 397.8+/-236.7 vs. 491.5+/-208.4; and 133.6+/-97.4 vs. 198.5+/-91.6 respectively; p<0.05 for all). Significant negative correlations were observed between serum FSH, LH and testosterone levels and most of the HRV parameters. CONCLUSIONS: Deficiency in the male hypothalamo-pituitary-gonadal axis seems to adversely affect cardiac autonomic modulation with increased sympathetic and decreased parasympathetic components of HRV.