Abstract. Heart rate variability (HRV) is a biomarker used to reflect both healthy and pathological state(s). The effect of the menstrual cycle and menstrual cycle phases (follicular, luteal) on HRV remains unclear. Active eumenorrheic women free from exogenous hormones completed five consecutive weeks of daily, oral basal body temperature (BBT) and HRV measurements upon waking. Descriptive statistics were used to characterize shifts in the HRV measures: standard deviation of NN intervals (SDNN), root mean square of successive difference (rMSSD), high (HF) and low frequency (LF) across the menstrual cycle and between phases. All HRV measures were assessed by medians ( Mdn), median difference of consecutive days ( Mdn∆) and variance. Seven participants ( M ±  SD; age: 28.60 ± 8.40 year) completed the study with regular menstrual cycles (28.40 ± 2.30 days; ovulation day 14.57 ± 0.98 day). Median rMSSD displayed a nonlinear decrease across the menstrual cycle and plateau around the day of ovulation. A negative shift before ovulation in Mdn∆, rMSSD, SDNN, and LF as well as peak on luteal phase Day 4 in rMSSD and SDNN was observed. Median variance increased in rMSSD (150.06 ms2) SDNN (271.12 ms2), and LF variance (0.001 sec2/Hz) from follicular to luteal phase. Daily HRV associated with the parasympathetic nervous system was observed to decrease nonlinearly across the menstrual cycle.