The purpose of the present study was to determine whether there is a menstrual cycle effect on heart rate variability. Ten healthy regularly cycling females (age 19‐23 years) were studied during the follicular phase (FP) and luteal phase (LP) of menstrual cycle over two month. We found significant changes in heart rate (65,35±0,68 beats/min in FP vs 73,18±0,92 beats/min in LP, p<0,0005), AMo and stress index during the menstrual cycle with a minimum in the follicular phase (36,81±1,14 % and 76,86±5,74 p.d.u. respectively) and maximum in the luteal phase (42,05±1,27 % and 107,70±7,77 p.d.u. respectively, p<0,003). The HF and LF components decreased more during the luteal phase (655,56±46,64 ms2 and 981,85±66,64 ms2 respectively) than during the follicular phase (997,42±83,36 ms2 and 1524,66±145,17 ms2 respectively, p<0,05). In the follicular phase SDNN, pNN50, MxDMn were significantly higher (0,057±0,002 s, 41,49±1,79 % and 0,333±0,012 s respectively) than in the luteal phase (0,051±0,002 s, 29,73±1,88 % and 0,303±0,012 s respectively, p<0,05). Furthermore, the VIK was higher in the luteal phase compared to the follicular phase (p=0,003). These findings indicate that sympathetic nervous activity in the luteal phase is greater than in the follicular phase, whereas parasympathetic nervous activity is predominant in the follicular phase. A difference of the balance of ovarian hormones may be responsible for these changes of autonomic functions during the menstrual cycle.