Spectral analysis was used to assess heart rate variability in consecutive 5-min epochs during the night in 12 normal adults. Simultaneous time coding of EEG and digitized EKG allowed examination of heart rate variability as a function of sleep stage, time of night and presence of EEG arousal. The results replicated previous studies in showing increases in high frequency components and decreases in low frequency components of heart rate variability across NREM sleep stages and opposite changes in REM sleep and wake. These results are consistent with sympathetic nervous system activation during REM sleep and wake periods. The shift in heart rate variability seen during REM sleep began in NREM sleep several minutes prior to standardly scored REM and often continued beyond the end of REM sleep. EEG arousals during Stage 2 and to some extent REM sleep were also associated with changes in heart rate variability which were consistent with sympathetic activation. An examination of beat to beat intervals in proximity to EEG arousals showed heart rate acceleration at least 10 beats prior to the EEG arousal. The arousal data along with Stage 2 sleep transition data support the contention that increases in central nervous system sympathetic activity precede and possibly play a role in the initiation of REM sleep and arousals during sleep.