UNLABELLED: Chagas disease (CD) is an infection caused by the protozoan flagellate Trypanosoma cruzi, and transmitted by insects of the genera Triatoma, Rhodnius and Panstrongylus. The heart is affected to varying degrees by inflammatory and destructive lesions in atrial and ventricular myocardial fibers. Several studies have demonstrated the benefits of exercise in patients with congestive heart failure (CHF), including reduced sympathetic tone and increased parasympathetic tone, the result of reduced epinephrine and norepinephrine levels, both at rest and during exercise, including at submaximal levels. It has been hypothesized that the increase in sympathetic arousal during exercise improves peripheral muscle metabolism. OBJECTIVES: The objectives of this study were to select patients with chronic Chagas cardiomyopathy (CCC) with dysautonomia on 24-h Holter monitoring, assess autonomic function after rehabilitation, and determine whether it resulted in reduced daytime levels of SDNN and increased daytime and nighttime levels of pNN50 and rMSSD. METHODS: We analyzed time-domain indices of heart rate variability through 24-h Holter monitoring before and after a supervised exercise program. We studied 18 CCC patients (five men), mean age 57.33±9.73 years, followed at the CD outpatient clinic of the National Institute of Cardiology and IPEC/Fiocruz in Rio de Janeiro, Brazil, between April 2009 and November 2010. The following tests were used to assess the severity of CCC: clinical examination, functional evaluation by cardiopulmonary stress testing, electrocardiogram and conventional Doppler echocardiography. The exams were performed within a month of the start and end of the exercise program, which consisted of 60-min sessions of aerobic exercise on a treadmill and resistance training three times a week for six months. The goal was to reach the patients' heart rate target zone during training, and their rating of perceived exertion was assessed by the modified Borg scale. RESULTS: There were no statistically significant differences (p>0.05) in SDNN, pNN50 and rMSSD, probably due to the large standard deviation observed, patients' poor adherence to the program and their low socioeconomic status, resulting in a small sample, and the short duration of the program. CONCLUSION: Heart rate variability parameters in patients with CCC did not undergo statistically significant changes after a six-month cardiac rehabilitation program.