The objective of this systematic review is to summarize and critically assess the effects of yoga on heart rate variability (HRV). Nine databases were searched from their inceptions to June 2014. We included randomized clinical trials (RCTs) comparing yoga against any type of control intervention in healthy individuals or patients with any medical condition. Risk of bias was assessed using the Cochrane criteria. Two reviewers performed the selection of studies, data extraction, and quality assessments independent of one another. Fourteen trials met the inclusion criteria. Only two of them were of acceptable methodological quality. Ten RCTs reported favourable effects of yoga on various domains of HRV, whereas nine of them failed to do so. One RCT did not report between-group comparisons. The meta-analysis (MA) of two trials did not show favourable effects of yoga compared to usual care on E:I ratio (n = 61, SMDs = 0.63; 95% CIs [-0.72 to 1.99], p = 0.36; heterogeneity: r(2) = 0.79, ?(2) = 5.48, df = 1, (p = 0.02); I(2) = 82%). The MA also failed to show statistically significant differences between the groups regarding the 30:15 ratio (n = 61, SMDs = 0.20; 95% CIs [-0.43 to 0.84], p = 0.53; heterogeneity: r(2) = 0.07, ?(2) = 1.45, df = 1, (p = 0.23); I(2) = 31%). The data from the remaining RCTs were too heterogeneous for pooling. These results provide no convincing evidence for the effectiveness of yoga in modulating HRV in patients or healthy subjects. Future investigations in this area should overcome the multiple methodological weaknesses of the previous research.