Heart rate variability, a noninvasive marker of parasympathetic activity, diminishes with aging and is augmented after exercise training. Whether habitual exercise over time can attenuate this loss is unknown. This cross-sectional investigation compared 72 male runners, aged 15 to 83 to 72 age- and weight-matched sedentary control subjects for the amplitude of their heart rate variability. Heart rate variability was assessed during rest while subjects were breathing at a rate of 6 breaths per minute and at an augmented tidal volume (tidal volume = 30% of vital capacity). Fitness levels were assessed with on-line, open-circuit spirometry while subjects were performing an incremental stress test. Overall results between the two groups showed that the physically active group had significantly higher fitness levels (p < 0.001), which were associated with significantly higher levels of heart rate variability, when compared with their sedentary counterparts (p < 0.001). These findings provide suggestive evidence for habitual aerobic exercise as a beneficial modulator of heart rate variability in an aging population.