The idea of chakras as understood in Eastern philosophy does not exist in medical science. In Eastern thought, the chakras are thought to be levels of consciousness, and states of the soul, and 'proving' the existence of chakras is asking to 'prove' the existence of a soul. A mystic deals with these occult concepts on the occult plane, as a model for their own internal experience, and when talking about 'energy centres', they are generally talking about subtle, spiritual forces, which work on the psyche and spirit, not about physical, electrical, or magnetic fields. 

The primary importance and level of existence of chakras is therefore posited to be in the psyche. However, there are those who believe that chakras have a physical manifestation as well. Although there is no evidence that Indian mystics made this association themselves, it is noted by many that there is a marked similarity between the positions and roles described for chakras, and the positions and roles of the glands in the endocrine system, and also by the positions of the nerve ganglia (also known as "plexuses") along the spinal column, opening the possibility that two vastly different systems of conceptualization have been brought to bear to systemize insights about the same phenomenon. By some, chakras are thought of as having their physical manifestation in the body as these glands, and their subjective manifestation as the associated psychological and spiritual experiences. 

Indeed, the various hormones secreted by these glands do have a dramatic effect on human psychology, and an imbalance in one can cause a psychological or physical imbalance in a person. Whether these changes in body state have a bearing on spiritual matters is a subject of dissent even among the Indian theorists, and the different systems of conceptualization, Indian and Western, make only a partial convergence in this case. 

Perhaps the most psychologically dramatic and potent secretion of these glands is the psychedelic drug DMT (which is thought to be synthesized by the pineal gland, corresponding to the brow chakra). At least in the West, some individuals have sought spiritual breakthroughs through the use of such chemical aids, occasionally referred to as entheogens in this context. (See for example: Aldous Huxley, The Doors of Perception, a classic of new-age spirituality.)