Obstructive sleep apnea seems to have an important influence on the autonomic nervous system. In this study, we assessed the relations of sleep apnea-related parameters with 24-hour heart rate variability (HRV) in a large population of young and healthy adults. Participants aged 25 to 41 years with a body mass index <35 kg/m(2) and without known obstructive sleep apnea were included in a prospective population-based cohort study. HRV was assessed using 24-hour electrocardiographic monitoring. The SD of all normal RR intervals (SDNN) was used as the main HRV variable. Apnea-Hypopnea Index (AHI) and oxygen desaturation index (ODI) were obtained from nighttime pulse oximetry with nasal airflow measurements. We defined sleep-related breathing disorders as an AHI >/=5 or an ODI >/=5. Multivariable regression models were constructed to assess the relation of HRV with either AHI or ODI. Median age of the 1,255 participants was 37 years, 47% were men, and 9.6% had an AHI >/=5. Linear inverse associations of SDNN across AHI and ODI groups were found (p for trend = 0.006 and 0.0004, respectively). The beta coefficients (95% CI) for the relation between SDNN and elevated AHI were -0.20 (-0.40 to -0.11), p = 0.04 and -0.29 (-0.47 to -0.11), p = 0.002 for elevated ODI. After adjustment for 24-hour heart rate, the same beta coefficients (95% CI) were -0.06 (-0.22 to 0.11), p = 0.51 and -0.14 (-0.30 to 0.01), p = 0.07, respectively. In conclusion, even early stages of sleep-related breathing disorders are inversely associated with HRV in young and healthy adults, suggesting that they are tightly linked with autonomic dysfunction. However, HRV and 24-hour heart rate seem to have common information.