Ajna chakra is often directly related to the physical pineal gland, the pea-sized endocrinal gland located in the centre of the head. In fact, they are often regarded as one and the same thing. This is rather an over-simplification. The difference should be clearly understood. The pineal gland refers to the physical body; the ajna chakra spans the chasm between the physical and the most subtle psychic realms. In fact, ajna chakra leads beyond the psychic realms via sushumna. It seems likely that the pineal gland is part of ajna chakra; it is that part of ajna chakra that acts in the physical body. But ajna chakra as a whole goes much deeper. Ajna can be compared to a mountain in the sea; the peak, the island that can be seen above the surface of the sea, is the pineal gland. The rest of ajna chakra, the base of the mountain, goes much, much deeper than can be seen with normal perception.
The physiological functions of the pineal gland have baffled medical scientists for centuries. Even today it is not very well understood, though gradually it is divulging its secrets. It seems that the pineal gland acts as a biological clock which regulates man’s activities according to outside circumstances. It has been found that the eyes and the pineal gland are connected via the sympathetic nervous system; and that light entering the eyes directly influences some of the functions of the pineal. The pineal gland in turn regulates the whole sympathetic nervous system which greatly controls human behaviour. Thus cosmic rhythms, such as night and day, the moon and sun cycle and so forth, influence man’s behaviour via the pineal gland. Melatonin and other hormones are produced in response to outside stimuli; these in turn produce changes in sexual behaviour, menstrual cycles, nervous energy and other biological rhythms of man. Thus it seems that the pineal gland acts like a radio antenna, which picks up outside signals and regulates man’s behaviour accordingly.
It is interesting to note that the pineal gland is not directly connected to the brain, at least as far as we can tell by current scientific research. It therefore seems that man’s behaviour is influenced by two systems – the pineal gland and the mind acting through the brain.
Besides being a link between the outer material environment and man, it seems that the pineal gland also acts as a gateway to the more subtle realms of the psyche. The pineal gland is a physical transducer between the physical and psychic planes. Thus psychic changes can induce corresponding physical changes via the pineal gland. Conversely, physical, chemical or any other stimulation of the pineal gland can bring about repercussions in the psyche. This is indicated by practices of trataka (blinkless gazing) where the ajna chakra can be awakened via the eyes and pineal gland; the practice of sirshasana can also induce psychic changes, though to a lesser degree, by increasing the blood supply to the pineal gland. Various drugs also bring about psychic changes; it is possible that they directly influence the chemistry of the pineal gland. Thus it appears that the pineal gland is a switch or a sluice gate which restricts or opens up psychic awareness. Direct stimulation of the pineal gland by various yogic practices can help to awaken the ajna chakra.
To summarize: the pineal gland is a material body that seems to be a physical manifestation of the ajna chakra. They are not the same, for the ajna chakra, while including the pineal gland, dives much deeper into the more subtle levels of being. The ajna is the link between the physical level of being and the sahasrara.