BACKGROUND: High intensity interval training (HIIT) has been used as a cardiovascular exercise strategy to promote greater adherence in cardiovascular rehabilitation. However, little is known about the effect of this training modality on cardiac autonomic control. OBJECTIVE: To perform a systematic review to evaluate the effects of HIIT on cardiac autonomic responses in humans. METHODS: PEDro, SCOPUS and PubMed were searched from the inception to March 29th, 2018. Moreover, the methodological quality and statistical reporting from all eligible clinical trials were assessed by the PEDro scale. The articles were eligible if: The primary objective was related to the effects of HIIT on the cardiac autonomic nervous system. Outcomes evaluated were indirect measures of cardiac autonomic control, represented by HRV indexes. RESULTS: The search strategies resulted in 339 citations and 2 additional citations were identified through other sources. After deleting the duplicate articles and revising the full text, 6 articles were included. Overall, the results showed an improvement in parasympathetic and/or sympathetic modulation after HIIT, when evaluated by linear and non-linear indexes of HRV. CONCLUSIONS: HIIT is a promising tool to improve the cardiac autonomic control, with more recommendation in healthy individuals and patients with metabolic syndrome.