Cardiac autonomic regulation across the menstrual cycle is highly individual: evidence from phase-aligned cyclic generalized additive mixed models.

Cardiac autonomic regulation, indexed by heart rate variability (HRV), is hypothesized to fluctuate across the menstrual cycle. Empirical findings remain inconsistent, likely due to sparse phase-based sampling and limited consideration of interindividual variability. This study examined cyclic HRV trajectories using longitudinal monitoring and phase-aligned cycle time scaling (PACTS) to distinguish population-level from individual-specific patterns and to evaluate associations with well-being. Daily HRV (smartphone photoplethysmography) and well-being were collected in 21 naturally cycling women. Cycle time was aligned using PACTS, with ovulation set to 0 and follicular and luteal phases rescaled to a common -1 to +1 interval. Vagally mediated HRV was indexed using log-transformed root mean square of successive differences [ln(RMSSD)] and the coefficient of variation (CV) of ln(RMSSD), calculated from a centered rolling window. Cyclic generalized additive mixed models separated population-level smooths from participant-specific cyclic deviations. Associations between well-being (sleep quality, stress, fatigue, and muscle soreness) and HRV were examined using mixed-effects models distinguishing within- and between-person effects. For ln(RMSSD), the population-level cyclic trajectory was flat and nonsignificant, whereas participant-specific cyclic deviations were significant, indicating pronounced interindividual heterogeneity despite a stable average pattern. Similar results were observed for CV ln(RMSSD). Within-person analyses showed that poorer sleep quality, higher stress, and greater fatigue were associated with lower ln(RMSSD), whereas between-person differences were unrelated to mean HRV. Increases in stress and muscle soreness were associated with modest increases in HRV fluctuations. When menstrual cycle timing is precisely aligned to ovulation, vagally mediated HRV shows no consistent population-level rhythm but marked individual-specific dynamics, strongly modulated by day-to-day well-being.NEW & NOTEWORTHY Using dense longitudinal monitoring and ovulation-aligned cycle scaling, this study shows that vagally mediated heart rate variability does not follow a consistent population-level rhythm across the menstrual cycle. Instead, cardiac autonomic regulation exhibits pronounced individual-specific cyclic patterns and is strongly influenced by day-to-day fluctuations in subjective well-being. These findings help explain previously inconsistent menstrual cycle effects on heart rate variability.