Autonomic modulation and cardiorespiratory variables are influenced by numerous factors, including anthropometric variables. We investigated autonomic recovery following aerobic exercise in healthy men with different waist-stature ratio (WSR) values. The study was conducted with 52 healthy men aged 18 to 30 years, divided into groups according to the WSR: G1 - between 0.40 and 0.449 (N = 19), G2 - between 0.45 and 0.50 (N = 28) and G3 - between 0.5 and 0.56 (N = 5). The subjects endured 15 minutes seated and at rest followed by an aerobic exercise and then remained seated for 60 minutes and at rest during recovery from exercise. Heart rate (HR) variability (HRV) (rMSSD, SD1, HF [ms2]) and cardiorespiratory variables were analyzed before and after exercise. Recovery of respiratory rate, diastolic blood pressure, SD1 and HF indices were delayed in G2. G3 presented delayed recovery after the maximal effort test while no difference with G2 was noted in the moderate intensity. Correlation and linear regression analysis indicated association of WSR, body mass index and waist circumference with HRV indices in the recovery from aerobic exercise (45 to 60 minutes after exercise) in G2. In conclusion, healthy men with higher WSR accomplished delayed autonomic recovery following maximal effort exercise.