Yogic breathing is a unique method for balancing the autonomic nervous system and influencing psychologic and stress-related disorders. Part I of this series presented a neurophysiologic theory of the effects of Sudarshan Kriya Yoga (SKY). Part II will review clinical studies, our own clinical observations, and guidelines for the safe and effective use of yoga breath techniques in a wide range of clinical conditions. Although more clinical studies are needed to document the benefits of programs that combine pranayama (yogic breathing) asanas (yoga postures), and meditation, there is sufficient evidence to consider Sudarshan Kriya Yoga to be a beneficial, low-risk, low-cost adjunct to the treatment of stress, anxiety, post-traumatic stress disorder (PTSD), depression, stress-related medical illnesses, substance abuse, and rehabilitation of criminal offenders. SKY has been used as a public health intervention to alleviate PTSD in survivors of mass disasters. Yoga techniques enhance well-being, mood, attention, mental focus, and stress tolerance. Proper training by a skilled teacher and a 30-minute practice every day will maximize the benefits. Health care providers play a crucial role in encouraging patients to maintain their yoga practices.