The aetiology of impairments in autonomic modulation of heart rate variability (HRV) in polycystic ovary syndrome (PCOS) remains unclear, as does the impact of aerobic physical training (APT) on controlling endocrine-metabolic disorders and HRV. This is because these women often present excess body fat. Therefore, we assessed whether the dysregulation in autonomic modulation of HRV in women with PCOS is due to endocrine-metabolic disorders and whether the combination of excess body fat with endocrine-metabolic disorders amplifies cardiovascular autonomic deficits. We also investigated whether APT positively influences autonomic modulation of HRV in PCOS.