Spectral analysis of heart rate variability (HRV) is commonly employed to track changes in autonomic nervous system and respiratory activity during sleep. However, conventional HRV spectral indices can be seriously confounded by inter-subject differences or intra-individual changes in ventilation and ventilatory pattern, especially in subjects with obstructive sleep apnea syndrome (OSAS). We highlight the approach we have undertaken to circumvent this problem by introducing "respiration-adjusted" spectral indices of HRV. Since fluctuations in sleep state also affect HRV considerably, we describe a method for combining the information derived from sleep staging and the information derived from cardiorespiratory measurements. We also introduce a new complementary index of autonomic function, BRS(PTT), based on measurements of heart period and pulse transit time. We demonstrate that this surrogate measure of baroreflex gain correlates well with the corresponding measures of baroreflex sensitivity based on noninvasive blood pressure measurements. Our experience to date suggests that BRS(PTT), along with respiration-adjusted spectral measures of HRV, are useful as clinical tools for assessing autonomic dysfunction in OSAS.