Stroke has been associated with cardiac autonomic impairment due to damage in central nervous system. Dysfunction in heart rate variability (HRV) may reflect dysfunction of the autonomic nervous system. Aerobic training has been used in the rehabilitation procedure of patients, due to improvement of aerobic function and other beneficial effects as increased recruitment of motor units, favoring the development of muscle fibers. The purpose of this study was to evaluate the cardiac autonomic modulation in patients with stroke before, during, and after an acute bout of aerobic exercise. The heart rate of 38 stroke patients was recorded using a heart rate (HR) monitor and the data were used to assess cardiac autonomic modulation through HRV analysis. The patients were in supine position and remained at resting condition (R) for 10 min before starting the experiment. Afterwards, they were submitted to walking exercise (E) on a treadmill until achieve 50-70% of maximum heart rate. After 30 min of aerobic exercise, the subjects were advised to remain in supine position for additional 30 min in order to record the HR during the recovery (RC) period. The recordings were divided in three periods: RC1, immediately after the end of exercise bout, RC2, between 12 and 17 min of recovery, and RC3, at the final 5 min of recovery. A significant decrease was observed during exercise in the MeanRR index (577.3±92 vs. 861.1+109), RRtri (5.1±2 vs. 9.1±3), high frequency component (11.2±4 vs. 167±135 ms) and SD1 (5.7±2 vs. 16.9±7 ms) compared to resting values. The SDNN index reduced during E (27.6±19) and RC1 (29.9±11), RC2 (27.9±9) and RC3 (32.4±13) compared to resting values (42.4±19). The low frequency component increased during E (545±82), but decreased during RC1 (166.3±129), RC2 (206.9±152), and RC3 (249.5±236) compared to R levels (394.6±315). These findings suggest that stroke patients showed a reduced HRV during and at least 30 min after exercise, due to an autonomic imbalance reflected by increased indexes that represent the sympathetic nervous system.