Heart rate variability has been proposed as an indicator of cardiovascular health. Since women have a lower cardiovascular risk, we hypothesized that there are gender differences in autonomic modulation. In 276 healthy subjects (135 women, 141 men) between 18 and 71 years of age, 24 h heart rate and heart rate variability were determined. All heart rate variability parameters, except for pNN50 and high frequency power, were higher in men. After adjustment for heart rate, we obtained gender differences for: the standard deviation (P=0.049), the standard deviation of the 5 min average (P=0.047), low frequency power (absolute values, P=0.002; normalized units, P<0.001) and ratio low frequency/high frequency (P<0.001). There were no significant gender differences in heart rate variability parameters denoting vagal modulation. Gender differences were confined to age categories of less than 40 years of age. The majority of heart rate variability parameters decreased with age. Only in men, was a higher body mass index associated with a higher heart rate and with lower heart rate variability parameters (P<0.001). Cardiac autonomic modulation as determined by heart rate variability, is significantly lower in healthy women compared to healthy men. We hypothesize that this apparently paradoxical finding may be explained by lower sympathetic activity (low frequency power) in women. This may provide protection against arrhythmias and against the development of coronary heart disease.