Persons with Down syndrome (DS) are at high risk for cardiovascular morbidity and mortality, and there is compelling evidence of autonomic dysfunction in these individuals. The main purpose of this study was to determine whether a combined aerobic and resistance exercise intervention produces similar results in cardiac autonomic function between adults with and without DS. Twenty-five participants (13 DS; 12 non-DS), aged 27-50 years, were included. Aerobic training was performed 3 days/week for 30 min at 65-85% of peak oxygen uptake (VO[subscript 2peak]). Resistance training was prescribed for 2 days/week and consisted of two rotations in a circuit of 9 exercises at 12-repetition-maximum. There was a significant improvement in the VO[subscript 2peak] and muscle strength of participants with and without DS after training. Heart rate recovery improved at 1 min post-exercise, but only in participants with DS. Both groups of participants exhibited a similar increase in normalized high frequency power and of decrease in normalized low frequency power after training. Therefore, 12 weeks of exercise training enhanced the heart rate recovery in adults with DS, but not in those without DS. Contrasting, the intervention elicited similar gains between groups for cardiovagal modulation. (Contains 3 tables and 2 figures.)