OBJECTIVE Cyclic alternating pattern (CAP) consists of arousal-related phasic events while the complementary condition, non-CAP (NCAP), is characterized by a rhythmic background activity, reflecting a condition of stable arousal, during non-REM sleep. The arousal swings that accompany the appearance of CAP on the EEG are associated with transient variations of muscle tone and autonomic activities, including heart rate (HR). The aim of our study was to evaluate HR variability in relation to CAP during non-REM sleep in healthy adults. METHODS Ten healthy subjects (mean age = 28.1 years) underwent 8 h polysomnography. HR variations were measured by power spectrum analysis. The ECG signals were segmented in correspondence of the different sleep stages and different CAP conditions. RESULTS A significant difference between CAP and NCAP conditions was found in low frequency (LF) component (increased in CAP) and high frequency (HF) component (decreased in CAP). LF/HF ratio was increased in CAP. CONCLUSIONS Physiological fluctuations of the EEG arousal level influence cardiac autonomic activity in normal subjects. The studies on nocturnal variation in sympathetic and vagal tone should take in account the microstructural sleep changes, other than the conventional polysomnographic parameters.