This study investigated the fluctuations of autonomic nervous activities during the menstrual cycle. Twenty college females were tested for cardiovascular reactivity to mental challenge during both follicular and luteal phases across two menstrual cycles. Power spectral analysis of heart rate variability (HRV) was used to examine the autonomic nervous activities. At baseline, although heart rate and blood pressure did not differ across the menstrual cycle, the low-frequency (LF) component in the HRV was higher and the high-frequency (HF) component in the HRV was lower during the luteal phase than during the follicular phase. The LF/HF ratio was also significantly greater in the luteal phase. These data suggest that sympathetic nervous activities are predominant in the luteal phase as compared with follicular phase. In addition, the power spectral analysis of HRV has more sensitivity than heart rate or blood pressure in assessing the slight fluctuations of autonomic nervous activities during the menstrual cycle.