We examined the effects of sleep stages and sleep-disordered breathing (SDB) on autonomic modulation in 700 children. Apnea hypopnea index (AHI) during one 9 h night-time polysomnography was used to define SDB. Sleep stage-specific autonomic modulation was measured by heart rate variability (HRV) analysis of the first available 5 min RR intervals from each sleep stage. The mean [standard deviation (SD)] age was 112 (21) months (49% male and 25% non-Caucasian). The average AHI was 0.79 (SD = 1.03) h(-1), while 73.0%, 25.8% and 1.2% of children had AHI <1 (no SDB), 1-5 (mild SDB) and >or=5 (moderate SDB), respectively. In the no SDB group, the high frequency (HF) and root mean square SD (RMSSD) increased significantly from wake to Stage 2 and slow wave sleep (SWS), and then decreased dramatically when shifting into rapid eye movement (REM) sleep. In the moderate SDB group, the pattern of HRV shift was similar to that of no SDB. However, the decreases in HF and RMSSD from SWS to REM were more pronounced in moderate SDB children [between-group differences in HF (-24% in moderate SDB versus -10% in no SDB) and RMSSD (-27% versus -12%) were significant (P < 0.05)]. The REM stage HF is significantly lower in the moderate SDB group compared to the no SDB group [mean (standard error): 4.49 (0.43) versus 5.80 (0.05) ms(2), respectively, P < 0.05]. Conclusions are that autonomic modulation shifts significantly towards higher parasympathetic modulation from wake to non-rapid eye movement sleep, and reverses to a less parasympathetic modulation during REM sleep. However, the autonomic modulation is impaired among children with moderate SDB in the directions of more reduction in parasympathetic modulation from SWS to REM sleep and significantly weaker parasympathetic modulation in REM sleep, which may lead to higher arrhythmia vulnerability, especially during REM sleep.