Regular exercise training is considered to be capable of beneficially modifying the autonomic balance in healthy subjects. We studied the association between vagal HRV indexes and the level of physical activity in Chagas disease patients and control subjects. Although in controls habitual physical activity was closely associated with vagal HRV indexes, no relationship was found between IPAQ scores and HRV indexes in a Chagas disease group, suggesting that Chagas dysautonomia disrupted this potentially beneficial association.