Introduction: The cardiac form is the main responsible for morbidity and mortality of Chagas disease (ChD), given its prevalence and unpredictable clinical evolution. A great part of ChD mortality occurs due to sudden ventricular arrhythmias, and the frequently observed autonomic dysfunction may be associated with unfavorable outcomes. We aimed to evaluate the predictive value of autonomic dysfunction indexes in ChD patients. Methods: The Bambuí Study of Aging is a prospective cohort of residents ≥60 years at study onset (1997), living in the southeastern Brazilian city of Bambuí (15,000 inhabitants). Consented participants underwent annual follow-up visits, and death certificates were tracked. For assessment of respiratory sinus arrhythmia (E:I ratio), patients were instructed to breathe deeply in a 10-second cycle (5 inhales and 5 exhales) while ECG was recorded. Heart rate variability indices (SDRR (standard deviation of adjacent RR intervals) and RMSSD (square root of the mean of the sum of squares of the differences between adjacent RR intervals)) were calculated using a computer algorithm, supervised by an independent cardiologist blinded to clinical data. Multivariable regression was performed to access the prognostic value of autonomic dysfunction indexes, expressed as tertiles, for all-cause mortality, after adjustment for demographic, clinical and ECG variables. Results: From 1,742 qualifying residents, 1,606 were enrolled, being 557 with positive ChD serology. Among these, mean age was 68 (64-74) years, and 32.5% were men. The most frequent ECG abnormality was right bundle branch block (23.2%). In 14 years, loss-to-follow-up was 7.9% and overall mortality was 51.9%. At total 321 ChD patients had valid autonomic indexes measurements. In univariate analyses, measurements of autonomic function predicted all-cause death: E:I ratio (HR: 1.20 (95% CI 1.09-1.33)), SDRR (HR: 1.26 (95% CI 1.14-1.40)) and RMSSD (HR: 1.12 (1.01-1.23)). After adjustment for sex, age and cardiovascular risk factors, none of these indexes remained as independent predictors of mortality. Conclusions: In a long-term cohort of elderly patients with ChD, abnormalities in autonomic function indexes were not independent predictors of 14-year mortality.