INTRODUCTION: Down syndrome (DS) results in many changes, including dysfunction in cardiac autonomic modulation. Heart rate variability (HRV) analysis evaluates the autonomic function and it is a predictor of adverse cardiovascular events. OBJECTIVE: To present results of a systematic review and a meta-analysis about heart rate variability in individuals with DS. METHOD: A systematic review was performed on PubMed, PubMed Central and Web of science databases. We included articles that exhibited all the terms: "Down Syndrome", "heart rate variability", "autonomic nervous system", "autonomic dysfunction" and "cardiac autonomic modulation". We conducted the meta-analysis to compare "DS" to "controls" during rest. Random effects models were used, as were appropriate tests for heterogeneity. RESULTS: From 271 studies, 13 were included in our review. These are conducted with volunteers from a wide age range, of either gender, and not taking medications. Meta-analysis displayed that there were no significant differences between the groups at rest, except the RMSSD, which revealed a significant (Z鈥?鈥?2.80, p鈥?鈥?.005) main effect (Hedge\'s g鈥?鈥?0.55, 95% CI [-0.93; -0.16]), indicating difference in individuals with DS compared with controls. CONCLUSION: There is autonomic dysfunction in individuals with DS, which may or may not be expressed at rest, but it is usually demonstrated in an autonomic task. Meta-analysis specified that there was no significant alteration between DS and the controls during rest, except RMSSD index which was lower in DS than controls. PROSPERO: CRD42017068647.