Chakras are a basic concept of yoga but typically are ignored by scientific research on yoga, probably because descriptions of chakras can appear like a fanciful mythology. Chakras are commonly considered to be centers of concentrated metaphysical energy. Although clear physiological effects exist for yoga practices, no explanation of how chakras influence physiological function has been broadly accepted either in the scientific community or among yoga scholars. This problem is exacerbated by the fact that yoga is based on subjective experience, and practitioners often shun objective descriptions. This essay builds on earlier work hypothesizing that intercellular gap junction connections provide a physiological mechanism underlying subtle energy systems described in yoga as well as other disciplines such as acupuncture. Three physical aspects of chakras are distinguished that are integrated through gap junction mechanisms and are proposed to have arisen during embryological development. Furthermore, electrical conductance associated with a high concentration of gap junctions could generate phenomena that, when subjectively experienced, have the radiant qualities attributed to chakras. This theory provides a scientific rationale for previously unexplained details of chakra theory and offers a new orientation to conceptualizing and studying such subjective phenomena.