PURPOSE: To investigate whether autonomic impairment post stroke modifies the influence of early aerobic training in relation to resting heart rate, peak workload and walking performance at the subacute stage post event. METHODS: Sixty-four patients after a first ischemic stroke were included and randomly assigned either to an aerobic training or to a control group. The training period lasted 8 weeks. Heart rate variability (HRV) parameters, aerobic and functional abilities were measured. RESULTS: Early aerobic exercise significantly improved endurance and walking performance in stroke patients (p< 0.05). A significant association was found between the HRV parameters two weeks post event and heart rate at rest and peak workload at the beginning of the program. No significant interaction effects between autonomic impairment and training on outcome measures were found. CONCLUSION: Early aerobic training resulted in positive effects on peak workload and walking parameters in stroke patients. No modification effect was found between HRV parameters and exercise on those parameters.