A broad range of mind-body therapies (MBTs) are used by the public today, and a growing body of clinical and basic sciences research has resulted in evidence-based integration of many MBTs into clinical practice. Basic sciences research has identified some of the physiological correlates of MBT practices, leading to a better understanding of the processes by which emotional, cognitive and psychosocial factors can influence health outcomes and well-being. In particular, results from functional genomics and neuroimaging describe some of the processes involved in the mind-body connection and how these can influence health outcomes. Functional genomic and neurophysiological correlates of MBTs are reviewed, detailing studies showing changes in sympathetic nervous system activation of gene transcription factors involved in immune function and inflammation, electroencephalographic and neuroimaging studies on MBT practices, and persistent changes in neural function and morphology associated with these practices. While the broad diversity of study designs and MBTs studied presents a patchwork of results requiring further validation through replication and longitudinal studies, clear themes emerge for MBTs as immunomodulatory, with effects on leukocyte transcription and function related to inflammatory and innate immune responses, and neuromodulatory, with effects on brain function and morphology relevant for attention, learning, and emotion regulation. By detailing the potential mechanisms of action by which MBTs may influence health outcomes, the data generated by these studies have contributed significantly towards a better understanding of the biological mechanisms underlying MBTs.