BACKGROUND: Heart rate variability (HRV) is a widely used non-invasive and quantitative marker of cardiac autonomic control. Elevated oxidative stress (OS) and reduced HRV have been proven in specific disease subsets. However, the impact of OS on the long-term heart rate dynamics of both conventional linear and non-linear origin in the general population is not known. METHODS: The 24-hour ambulatory electrocardiogram recordings and plasma 8-iso-prostaglandin F2alpha (8-iso-PGF2alpha) levels as an OS marker were acquired simultaneously in 71 consecutive patients. The conventional time and frequency domain HRV parameters and non-linear parameters were measured. RESULTS: The 8-iso-PGF2alpha is a significant determinant of most long-term conventional time and frequency domain HRV parameters and standard deviation (SD1, perpendicular to the line of identity; SD2, along the line of identity) descriptors from Poincare plot analysis, but not of non-linear complexity and fractal parameters. Patients with a high OS burden had lower absolute low-frequency and high-frequency powers during both the night and morning periods, with a significant decrease in high-frequency power in the morning. CONCLUSIONS: Oxidative stress is one of the significant determinants of the HRV. The severity of OS is reflected in the conventional time and frequency domain HRV parameters, but not in the non-linear measurements.