Meditation is a complex mental process that involves changes in cognition, sensory perception, emotions, hormones, and autonomic activity. Several brain regions are involved in these practices, particularly as they relate to improvements in brain function and psychological parameters, including the thalamus, frontal lobes, limbic system, and parietal lobes. Additionally, many different neurotransmitter systems are likely affected by meditation practices. Meditation programs have become widely used, either alone or combined with other therapies, for stress reduction depression, anxiety, and posttraumatic stress disorder. There has been an increasing understanding of the overall biological mechanism of meditation practices in terms of their effects on both the brain and body. Recent studies using clinical tools and functional neuroimaging have substantially augmented the knowledge of the biology of meditative practices. This chapter reviews current understanding regarding the physiological and neurophysiological effects of meditation practices as they pertain to brain health.