The purpose of this study was to determine if heart rate recovery (HRR) and heart rate variability (HRV) are related to maximal aerobic fitness and selected body composition measurements. Fifty men (age = 21.9 ± 3.0 years, height = 180.8 ± 7.2 cm, weight = 80.4 ± 9.1 kg, volunteered to participate in this study. For each subject, body mass index (BMI), waist circumference (WC), and the sum of skinfolds across the chest, abdomen, and thigh regions (SUMSF) were recorded. Heart rate variability (HRV) was assessed during a 5-minute period while the subjects rested in a supine position. The following frequency domain parameters of HRV were recorded: normalized high-frequency power (HFnu), and low-frequency to high-frequency power ratio (LF:HF). To determine maximal aerobic fitness (i.e., VO2max), each subject performed a maximal graded exercise test on a treadmill. Heart rate recovery was recorded 1 (HRR1) and 2 (HRR2) minutes during a cool-down period. Mean VO2max and BMI for all the subjects were 49.5 ± 7.5 ml·kg(-1)·min(-1) and 24.7 ± 2.2 kg·m(-2), respectively. Although VO2max, WC, and SUMSF was each significantly correlated to HRR and HRV, only SUMSF had a significant independent correlation to HRR1, HRR2, HFnu, LF:HF (p < 0.01). The results of the regression procedure showed that SUMSF accounted for the greatest variance in HRR1, HRR2, HFnu, and LF:HF (p < 0.01). The results of this study suggest that cardiovascular autonomic modulation is significantly related to maximal aerobic fitness and body composition. However, SUMSF appears to have the strongest independent relationship with HRR and HRV, compared to other body composition parameters and VO2max.