Research interest and participation in yoga for health-related outcomes are increasing worldwide, though the medical hypotheses and underlying mechanisms of yoga are infrequently discussed. This literature overview employs a systematic search to include articles of clinical investigation, synthesis or review that focus on potential underlying mechanisms for yoga’s effect on prevention and treatment of disease. Results indicate that empirical evidence and theories for yoga mechanisms are most prevalent in areas of hormonal regulation, sympathetic activity in the nervous system and the betterment of physical health attributes such as improved balance, flexibility, strength and cardiorespiratory health. Hypothetical effects of yoga on metabolism, circulation, behaviour, oxidative stress, inflammation and psychological thought processes are also examined, while new hypotheses in immunology, nerve conduction and bioelectromagnetism are reviewed. In context of the Medical Research Council’s complex intervention framework, methodological limitations and prospective research directions are discussed.