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Heightened sympathetic activity plays a role in the cardiovascular sequelae of obstructive sleep apnoea (OSA). Cardiac autonomic function may be assessed non-invasively by studying heart rate variability (HRV). The aim of the present study was to compare overnight HRV between a control group and a group of subjects with severe OSA. The potential confounding effects of age, sex, baseline autonomic status and sleep stage distribution were taken into account. Our prospective Holter study compared overnight (0030-0530 hours) HRV in 23 controls (apnoea hypopnoea index (AHI) = 5 ± 3 /h) and 23 subjects with severe OSA (AHI = 65 ± 23 /h), matched for age and sex and with a similar percentage of rapid eye movement sleep. The mean normal-to-normal RR interval (NN) was shorter in the OSA compared with control group (903 vs 1039 ms, respectively), whereas the other time-domain indices of HRV, as well as the classic frequency-domain indices, were similar. Essentially similar results were obtained hourly and when only subjects with high mean values of the standard deviation of all NN (≥ 90 ms) were evaluated. In the 0.01-0.06 Hz range corresponding to the typical OSA pattern of bradycardia-tachycardia termed cyclic variation of heart rate (CVHR), higher power was documented hourly in OSA, with a significant correlation between overnight power and both AHI and mean oxyhaemoglobin saturation. The percentage of NN > x ms different from the previous one (pNNx family) had no diagnostic value. The results of the present study suggest that NN may be the best index to quantify the overnight sympathovagal balance in OSA and that a spectral band overlapping the apnoea-related pattern of CVHR slightly improved the characterization of the apnoea-related HRV patterns., (© 2012 The Authors Clinical and Experimental Pharmacology and Physiology © 2012 Wiley Publishing Asia Pty Ltd.)