Mind-body interventions are beneficial in stress-related mental and physical disorders. Current research is finding associations between emotional disorders and vagal tone as indicated by heart rate variability. A neurophysiologic model of yogic breathing proposes to integrate research on yoga with polyvagal theory, vagal stimulation, hyperventilation, and clinical observations. Yogic breathing is a unique method for balancing the autonomic nervous system and influencing psychologic and stress-related disorders. Many studies demonstrate effects of yogic breathing on brain function and physiologic parameters, but the mechanisms have not been clarified. Sudarshan Kriya yoga (SKY), a sequence of specific breathing techniques (ujjayi, bhastrika, and Sudarshan Kriya) can alleviate anxiety, depression, everyday stress, post-traumatic stress, and stress-related medical illnesses. Mechanisms contributing to a state of calm alertness include increased parasympathetic drive, calming of stress response systems, neuroendocrine release of hormones, and thalamic generators. This model has heuristic value, research implications, and clinical applications.