Subtle Anatomy of the Brain

Art by Alex Grey

Physical anatomy and subtle anatomy are merely different angles on the human body. They work together in intricate ways to create your experience of this human life. There is no single cell, organ or energy center in the body that you could point to and say, “There! That spot is where I am.” Existence is a much more complicated network of physical components, empty space, consciousness, and soul.

The physical body without the animation of the soul is an empty shell. Understanding the physical and subtle structures and how they work together serves to enhance your practice of yoga and meditation.

When we apply a yogic perspective to anatomy and physiology, the elaborate design of our bodies can be seen as more than just a composite of chemicals, structures, and processes. We begin to understand the physical body as a vehicle to experience life.

Changing Our Habits

First you create your habits, often laid down early in life, and then the habits create you. A wide range of behaviors and patterns from favorite foods, to addiction to alcohol or sugar to how introverted or extroverted you are around strangers can all be traced to the habits laid down early in life.

Habits often get created to serve a particular function when we’re children but are no longer helpful as adults. Because habits are regulated through the endocrine system, they can be affected by eye focus, chanting, and breathwork. When we are ready for a new way of being, we must first shift the unhelpful permanent habits from childhood. That shift must begin with an adjustment of the hypothalamus, which in tum can shift deep, hard-wired  patterns in both the nervous and glandular systems.

Meditation works in a way that allows the brain and glands to relax and recharge. Repetition and rhythm are the soothing balms that repair the glands, which allow for a core-level shift in the body and consciousness. Over time, the applied discipline of meditation can unweave the traumas embedded in the physical and subtle anatomy to allow for a renewed sense of health, radiance, and balance.

Third Eye and Crown Chakra

The Third Eye is located between and just above the eyebrows. It contains the capacity for intuition and insight. When the Third Eye opens, the unseen becomes seen and a greater mental capacity is revealed. The Crown Chakra is located at the very top of the head. It is the Seat of the Soul and embodies the capacity to be authentic, blissful and to live with raised consciousness. It is the sweet spot that is activated as the Kundalini energy rises.

Both of these energy centers are intricately linked in with the glands, especially the glands deep in the brain. Often in meditation, the eyes are focused at the Third Eye or the crown of the head, which energetically charges up these centers. It also creates a pressure, via the optic nerve, which stimulates the pituitary, pineal, and hypothalamus glands.

The interplay of the pituitary, hypothalamus, pineal, and the ventricles of the brain contribute to the sense of deepening intuition that comes with a regular spiritual practice and the opening of the Third Eye. The expanded functioning of these glands also contributes to the regal acceptance of self and natural state of bliss that comes into play with a balanced Crown Chakra.

Yogi Bhajan taught that the glands operate in a rhythmic energetic frequency. The vibration (through the upper palate) of chanting and the pressure from the eye focus in meditation influence the glands to change, heal, and expand. These experiences can lead to a new level of sensitivity to environments, energies, and personalities.

Hemispheres of the Brain

The two sides of the brain have different capabilities and strengths.

Right Brain: Processes feelings and emotions; sees the big picture.

Left Brain: Processes facts, language, and details; sees the logistics.

Most people tend to be either more right-brained or more left-brained. However, for optimum function, both sides of the brain should work more or less equally well and communicate back and forth with ease. When the pattern of either left or right brain dominance is identified, yoga and meditation can be used to cultivate balance between the hemispheres. It is important that both sides of the brain are strong, healthy, balanced and communicating with each other.

Third Ventricle

The third ventricle is a fluid-filled space deep in the center of the brain that contains cerebrospinal fluid and is known in many yogic paths as the “cave of Brahma.” From a mystical perspective, it acts as a connecting point between the rational upper parts of the brain and the deeper survival based functions of the lower brain. The third ventricle is the space that connects the workings of the pineal and pituitary glands and the thalamus. It is possible that these structures work together in subtle ways to create the nectar of a spiritual practice. The third ventricle, like the center of a flower, is a space for many unique elements to come together and create sweetness.

Deep meditation stimulates change in this area. During meditation pearls of wisdom arise in this vestibule of ojas and cerebrospinal fluid. Physical and subtle anatomy merge in this space as the glands create the biochemical experience which correlates to the subtle experience of meditation. It is that sweet spot when the efforts of the dedicated yogi result in a pure glandular secretion. These Aha! moments of bliss happen amid the subconscious murmurings of the mind. The entire nervous system is soothed and rejuvenated as the newly invigorated cerebrospinal fluid circulates and bathes the nerves.

Our feelings of deep bliss, peace, and oneness that develop over many years of practice originate in this portal to universal knowledge, the third ventricle. It is the foundation of the body-mind-spirit connection. This cavern in the brain is the common space that allows for the transformation of consciousness.

1,000 Thoughts

Yogi Bhajan said you have1,000 thoughts per wink of the eye. Only a small percentage of those thoughts register on a conscious level. The other thoughts must go somewhere. They feed into the unconscious and subconscious minds. When practicing yoga and meditation you can start to identify those deep, subconsciously held thoughts that create your unconscious habits and patterns of being. Once they come into conscious awareness you can start processing  and healing those thoughts in order to make better choices.

The Vagus Nerve

The vagus nerve is one of twelve cranial nerves and is the only cranial nerve that leaves the cranium. It has the widest ranging influence of any nerve in the body. It takes a long and wandering path. The vagus nerve innervates multiple organs and crucial life systems, such as the heart, lungs, and digestive tract. It is part of the parasympathetic nervous system, which slows heart rate, controls blood pressure, and regulates breathing.

Research on the vagus nerve has revealed that it is also involved in our feelings of compassion, empathy, and goodness. Research participants with higher vagal nerve activity expressed higher feelings of altruism, love, and happiness. This is because of the vagus nerve’s influence on communication, heart rate, and its ability to trigger the release of oxytocin, a hormone responsible for feelings of bonding and connection. Research on children shows more cooperation and helpfulness when a child’s vagus nerve is more active.

This unique nerve holds the key to the ability to be present, aware, and compassionate. It is also one of the nerves most profoundly affected by the practice of yoga and meditation. Kundalini Yoga activates the vagus nerve with chanting, singing, whistling, pulling neck lock, eye focus (drishti), and practicing postures such as shoulder stand, plow pose, and cobra pose.

Vagus Nerve Exercise

Try this the next time you are feeling entitled or bent out of shape in some way. Imagine there is a gold chain connecting your chin and the little hollow in the center of the base of your neck and shorten the chain by pulling the chin down into an exaggerated Neck Lock. Take a few long deep breaths or try sitting in this posture for 11 minutes a day and see what changes arise in your attitudes. This posture is said to energize the vagus nerve, activating feelings of compassion, altruism, and perspective.

The physical and subtle design and structure of the human body are filled with messages, gifts, and lessons that can bring expanded awareness to life. When we look to the body to find those messages, all types of metaphors, reminders, and reassurances that this human life has meaning are revealed. Choose to look carefully at the body; hear its messages for they will bring you closer to your spiritual path.

©Enlightened Bodies: Exploring Physical and Subtle Human Anatomy by Japa Kaur and Nirmal Lumpkin

Enlighteded Bodies is available through KRI.

Originally Published

Art by Alex Grey

<i class="icon-cart"></i> STORE

Get YourFree Video

Enter your name and email below

Nameyour full name



Peace begins in me

By creating peace from within, we transform our lives and the world around us. Our platform is designed to connect with the highest aspect of our being, in order to tap into our full potential. As we learn to connect with our true identity rather than our external perceptions, we begin to experience the magic of ourselves in this extraordinary life.

Video Library



Nameyour full name
$ [field4 * field5]
Stripe Card Placeholder



45 minute practice.

Learn the tools and techniques to begin your journey.Some of these techniques may seem new or strange, but there is a deep science behind them that will contribute to your highest potential in transformation. Watch this before you begin the other videos. Enjoy!. FREE




9 minutes.

Learn the tools and techniques to begin your journey.Some of these techniques may seem new or strange, but there is a deep science behind them that will contribute to your highest potential in transformation. Watch this before you begin the other videos. Enjoy!. FREE