Heart rate variability (HRV) has been used as a proxy for health and fitness and indicator of autonomic regulation and therefore, appears well placed to assess the changes occurring with mind.-body practices that facilitate autonomic balance. While many studies suggest that yoga influences HRV, such studies have not been systematically reviewed. We aimed to systematically review all published papers that report on yoga practices and HRV. A comprehensive search of multiple databases was conducted and all studies that reported a measure of HRV associated with any yoga practice were included. Studies were categorized by the study design and type of yoga practice. A total of 59 studies were reviewed involving a total of 2358 participants. Most studies were performed in India on relatively small numbers of healthy male yoga practitioners during a single laboratory session. Of the reviewed studies, 15 were randomized controlled trials with 6 having a Jadad score of 3. The reviewed studies suggest that yoga can affect cardiac autonomic regulation with increased HRV and vagal dominance during yoga practices. Regular yoga practitioners were also found to have increased vagal tone at rest compared to non-yoga practitioners. It is premature to draw any firm conclusions about yoga and HRV as most studies were of poor quality, with small sample sizes and insufficient reporting of study design and statistical methods. Rigorous studies with detailed reporting of yoga practices and any corresponding changes in respiration are required to determine the effect of yoga on HRV.