In the ancient times the Pineal gland used to be a closed guarded secret. Only the initiated knew about it’s existence. Even the chakral system didn’t clearly denote it’s location leading to confusing the third eye with the “Ajna chakram” which is the pituitary body located just near the pineal gland between the eyebrows. Some vague revelation of this gland can however be found in religious symbolism and iconography. Like the Tibetan Thangkas where a blue dragon is seeking a blue stone. Or the Christian paintings that show the holy trinity with a blue stone. As noted in the Bible, 

“There they saw the God of Israel. Under his feet there seemed to be a surface of brilliant blue lapis lazuli, as clear as the sky itself.” – Exodus 24:10 (New Living Translation) 

While the pineal gland is the physical counterpart, all different esoteric doctrines attribute something sacred to it. According to more technical esotericism, in this pineal gland is located a “mental permanent atom”, a “seed of consciousness”, or the “Blue pearl”. This blue pearl is one of the permanent atoms, which is described in the works of Alice Bailey as, 

“These are 6 in number. Three relate to the spiritual triad, the mental, buddhic, and atmic permanent atoms. Three relate to the three atoms of the personality vehicle ― physical and astral permanent atoms, and the mental unit ― around which the bodies for a new incarnation are formed. They retain the vibratory rate of the individual at the moment of death, guaranteeing that the energetic evolutionary status thus far achieved will be carried over into successive lives.” 

All these permanent atoms are made of causal substance therefore imperishable and does not die with the demise of the physical body. The physical permanent atom is related to the physical body and it’s blueprint, the astral permanent atom is said to be related to the astral body. Them mental permanent atom, which is located in the pineal gland is the most important one, because it gives us access to the “kingdom of God” within, it links us with our Soul or our Solar Angel. This gland is related to our higher mental body. Mahatma Choa Kok Sui describes it as, 

“What exactly is the blue pearl? The blue pearl is the “seed of consciousness” or the mental permanent seed, found in the crown chakra, and located in the pineal gland. Through regular and prolonged meditation on the blue pearl or the seed of consciousness, one gradually experiences one’s true nature, which is called the “Buddha Nature” in Buddhism.”    – Master Choa Kok Sui, Om Mani Padme Hum: The Blue Pearl in the Golden Lotus, p. 55 

Authors like Manly P Hall and V.M Samael Aun Weor have also said similar things about this “blue pearl” or the mental permanent atom,

“The pineal gland is only five millimeters in diameter and is surrounded by fine, sand-like particles. The lotus flower of the pineal gland has one thousand petals that shine when forming the crown of the saints. An entire cosmic zodiac shines and gleams within the microcosmic human being. This is the glowing halo above the heads of the saints.” – V.M Samael Aun Weor 

From here we can conclue the pineal gland and the mental permanent atom located near it is related to the activation of the “thousand petalled crown energy centre”. While practices of meditation related to this mental permanent atom must be learned in the proper way from a reliable spiritual teacher, we can nevertheless tell, this gland is the secret to “intuition”, “clairvoyance” and all other higher faculties. In initiatic science when a student is accepted by a Holy Master, this same mental permanent atom is examined. This is where “the light in the head” shines and disciples who have a bright aura around this atom are chosen, while others are refused from entering the sacred door. Clairvoyant masters of the spiritual hierarchy have used this method to choose students to their ashrams. 

Therefore, it is very important for every practitioner to take good care of this gland. This gland is the link between our waking consciousness and the consciousness of the Christ within us. One way we can take a good care of this gland is by walking the path of reverence. By living a pure meditative life. By pure thoughts, our mental permanent atom is purified. So as we purify our thoughts, we indirectly influence our pineal gland and align it to the impulses coming from the soul. A lot of students will not pay much attention to this because it’s not laced with an exotic spiritual “technique”.  Many students who always look for a new technique or a new methods often forget these simple things thereby doing a great damage to themselves after doing dangerous occult practices. 

The Pineal gland is a natural organ of perception we all possess which is now atrophied. Apart from pure thinking, this gland is also related to our sexual glands. So students who live a chaste life, who conserve and transmute their sexual energy will also find their pineal gland awakened after living a pure life for a number of years. As Manly P Hall says, 

“The pineal gland is a link between the consciousness of man and the invisible worlds of Nature. Whenever the arc of the pituitary body contacts this gland there are flashes of temporary clairvoyance, but the process of making these two work together consistently is one requiring not only years bur lives of consecration and special physiological and biological training. This third eye is the Cyclopean eye of the ancients, for it was an organ of conscious vision long before the physical eyes were formed, although vision was a sense of cognition rather than sight in those ancient days.”
~Manly P. Hall