Abstract Introduction Pre-sleep stress or hyperarousal is a known key etiological component in insomnia disorder. However, physiological alterations during the sleep onset period are not well-understood. We aimed to characterize heart rate variability (HRV) in patients with insomnia during sleep onset. Methods Using data from the Sleep Heart Health Study at National Sleep Research Resource, we conducted a secondary analysis exploring HRV during the sleep onset period (defined as the time between lights-off and sleep onset) in patients with insomnia (IS group; n = 68) and comorbid obstructive sleep apnea (IS + OSA group; n = 135), compared with normal sleep controls (NSC group; n = 122). Overall group differences were tested using ANOVA. Post-hoc pairwise comparisons were conducted using the least significant difference (LSD) tests. Results During sleep onset, mean heart rates of the IS group (74.4±15.0 beats/min) and IS+OSA group (72.6±11.5 beats/min) were both significantly higher than the NSC group (69.7±9.4 beats/min, p=0.007 and p=0.044 respectively). Both the IS and IS+OSA groups showed lower heart rate variability compared to the NSC group, with significant differences in both time and frequency domains of HRV analysis including SDNN (p=0.002), RMSSD (p=0.035), pNN20 (p< 0.001), pNN50 (p=0.008), LnLF (p< 0.001), LnHF (p< 0.001). For all these measures, IS+OSA group had lower HRV compared to the IS group, although differences were not significant. When controlling for age, gender and BMI, and compared to the NSC group, IS group had significantly higher heart rates (β=4.8, p=0.008), and the IS+OSA group had significantly lower pNN20 (β=-0.039, p=0.002), pNN50 (β=-0.031, p=0.017) and LnHF (β=0.007, p=0.007). Conclusion Patients with insomnia had lower vagal activity during the sleep onset period, reflected in higher heart rates and lower heart rate variability. Such altered heart rate dynamics may serve as a physiological biomarker for insomnia during bedtime wakefulness, or as a potential tool to evaluate the efficacy of behavioral interventions which target bedtime stress. Support (if any) This research project was made possible by a grant from the American Academy of Sleep Medicine Foundation (PI: Yan Ma). We acknowledge the National Sleep Research Resource as the resource through which the Data/Datasets were obtained.