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Background The gender-specific influences of various confounding factors, including apnea, age, BMI, and cigarette consumption, on the function of the parasympathetic nerve system (PNS) during sleep in OSA patients has never been investigated. Methods One hundred ninety-seven males and 63 females with OSA were subjected to full PSG examinations including assessment of R-R intervals (RRIs) during an overnight ECG. The PNS-derived modulatory effect on the RRIs and the variability of this effect were quantified during REM and NREM using instantaneous time-frequency analysis with complex demodulation. The spectral domain with the maximum instantaneous amplitude in the high-frequency band between 0.15 and 0.4 Hz was defined as the main HF peak and used as a surrogate marker of PNS discharge. Based on density-spectrum-array maps of the main HF peaks (HF-DSA map), shifts in the central frequency of the main HF peak over time were continuously observed. When the main HF peaks on the HF-DSA maps maintained the same central frequency for more than 20 sec or 5 min, the PNS functions were considered to be “stable” or “very stable”, respectively. Results Apneas enhanced PNS-derived cardiac-modulation during REM in males, but more importantly, they made PNS-function unstable during both REM and NREM in males and during NREM in females. Aging blunted the PNS-derived cardiac-modulation during both REM and NREM regardless of gender, but aging had no impact on the stability of PNS-function. BMI blunted PNS-eliciting cardiac-modulation during REM in males and during NREM in both males and females. BMI made the PNS unstable during REM in females. Neither height nor cigarette consumption influenced any PNS-related parameter. Conclusions The PNS-derived cardiac-modulation was generally inhibited by aging and obesity, in which the effect of obesity was gender-specific. The PNS instability at nighttime was mainly induced by apneas but by obesity particularly during REM in females.