Sahasrara

Sahasrara or the crown chakra is said to be the chakra of consciousness, the master chakra that controls all the others. Its role would be very similar to that of the pituitary gland, which secretes hormones to control the rest of the endocrine system, and also connects to the central nervous system via the hypothalamus. The thalamus is thought to have a key role in the physical basis of consciousness. Symbolised by a lotus with a thousand petals. 

Ajna

Ajna or the third eye is linked to the pineal gland. Ajna is the chakra of time and awareness and of light. The pineal gland is a light sensitive gland, that produces the hormone melatonin, which regulates the instincts of going to sleep and awakening. It has been conjectured that it also produces trace amounts of the psychedelic chemical dimethyltryptamine. Symbolised by a lotus with two petals. 

(Note: some argue that the pineal and pituitary glands should be exchanged in their relationship to the Crown and Brow chakras, based on the description in Arthur Avalon's book on kundalini called Serpent Power or empirical research.) 

Vishuddha

Vishuddha or the throat chakra is said to be related to communication and growth, growth being a form of expression. This chakra is paralleled to the thyroid, a gland that is also in the throat, and which produces thyroid hormone, responsible for growth and maturation. Symbolised by a lotus with sixteen petals. 

Anahata

Anahata or the heart/emotions chakra is related to love, equilibrium, and well-being. It is related to the thymus, located in the chest. This organ is part of the immune system, as well as being part of the endocrine system. It produces T cells responsible for fighting off disease, and is adversely affected by stress. Symbolised by a lotus with twelve petals. 

Manipura

Manipura or the solar plexus chakra is related to energy, assimilation and digestion, and is said to correspond to the roles played by the pancreas and the outer adrenal glands, the adrenal cortex. These play a valuable role in digestion, the conversion of food matter into energy for the body. Symbolised by a lotus with ten petals. 

Swadhisthana

Swadhisthana or the sacral chakra is located in the groin, and is related to emotion, sexuality and creativity. This chakra is said to correspond to the testicles or the ovaries, that produce the various sex hormones involved in the reproductive cycle, which can cause dramatic mood swings. Symbolised by a lotus with six petals.

Muladhara

Muladhara or the base or root chakra is related to security, survival and also to basic human potentiality. This centre is located in the region between the genitals and the anus. Although no endocrine organ is placed here, it is said to relate to the inner adrenal glands, the adrenal medulla, responsible for the fight and flight response when survival is under threat. In this region is located a muscle that controls ejaculation in the sexual act. A parallel is drawn between the sperm cell and the ovum, where the genetic code lies coiled, and the kundalini. Symbolised by a lotus with four petals.