OBJECTIVE The purpose of the present study was to investigate autonomic tone during the follicular and luteal phases of the menstrual cycle using heart rate variability (HRV) and heart rate recovery (HRR) in healthy women. METHODS Thirty women aged 22-37 years with regular menstrual cycles were included in the study. The HRV and HRR were measured at the follicular and luteal phases. The HRV was obtained using the time domain method with 24-hour long-term recordings. For time domain analysis, the following were obtained: standard deviation of all normal sinus R-R intervals during 24 h (SDNN), mean of the standard deviation of all normal sinus R-R intervals for all 5-min segments (SDNN index), standard deviation of average normal sinus R-R intervals for all 5-min segments (SDANN), root mean square of the successive normal sinus R-R interval difference (rMSSD), and percentage of successive normal sinus R-R intervals longer than 50 ms (pNN50). The HRR was calculated at the first, second, and third minute of recovery after the cessation of peak exercise using a treadmill test. The paired sample t test was used for the comparison of both phases of the menstrual cycle. RESULTS The SDNN (136 ± 39 vs. 154 ± 32 ms; p = 0.015) and SDANN (122 ± 36 vs. 142 ± 36 ms; p = 0.004) were significantly lower during the luteal phase than during the follicular phase. The HRR, rMSSD, and pNN50 were not different between the 2 phases. CONCLUSIONS Parasympathetic tone markers of HRV and HRR were unaffected by the menstrual phase. Lower SDNN and SDANN during the luteal phase than during the follicular phase could have resulted from enhanced sympathetic activity during the luteal phase.