The identification of the chakras with the endocrine glands, throat with thyroid, brow with pituitary, crown with pineal, heart with thymus and so on, is one of the most widely repeated claims about them and is entirely modern; it originates with Leadbeater and the Theosophical writers of the early twentieth century, who were reaching for a physiological anchor at a time when endocrinology was new and exciting. It is not in the Sanskrit sources, which describe the centres within a subtle body, sukshma sharira, explicitly distinguished from the physical one.
There is no anatomical structure corresponding to a chakra, and no measurable phenomenon has been demonstrated at these sites; the practices associated with them are meditative, and claims that they diagnose or treat illness are not supported and should not displace medical care. The tradition's own framing, as a discipline of attention within a lineage, is both more modest and more interesting.
Sources Rainbow Body: A History of the Western Chakra System from Blavatsky to BrennanKurt Leland with The Serpent PowerSir John Woodroffe (Arthur Avalon)