There are fourteen departments of teaching dealing with different aspects and specialities of Ayurveda.

Department of Kayachikitsa (General Medicine)

Imparts training in the division of General Medicine in Ayurveda. In ancient times, the practice of Ayurveda comprised of the two schools of medicine and surgery. Kayachikitsa, representing the school of medicine forms the basis for all other branches of Ayurvedic treatment and hence this department lays the foundation for shaping a skilled Ayurvedic physician. Panchakarma (fivefold technique to detoxify the system) as well as Rasayana (Rejuvenative medicine) and Vajikarana (Reproductive Health) come within the purview of this department.  Training in this branch of Ayurvedic medicine equips the student to design a treatment protocol comprising of a range of internal and external medications as well as specialised therapies according to the nature of the disease and the patient. Ayurveda offers effective treatment for the management and control of chronic diseases like rheumatoid arthritis, osteoarthritis, psoriasis, eczema, bronchial asthma, paralysis, early stages of diabetes, gastrointestinal disorders, urinary tract infections and certain chronic infections.

Department of Shalya Tantra (Surgery)

Deals with the branch of Ayurvedic surgery and provides a basic understanding of the principles of modern surgery. Bone setting, application of medicated thread (ksharasutra) for management of haemorrhoids and fistula in ano, application of leech as well as management of cuts and wounds are the areas of strength in Ayurvedic surgery. Though modern surgery has advanced in leaps and bounds, the Ayurvedic principles of pre and post operative care still has relevance today.  Judicious application of Ayurvedic principles of surgical care can prevent complications and facilitate speedy recovery from surgical interventions. Ayurveda has historically made foundational contributions to the development of the branch of surgery. The practice of dissecting dead bodies to study anatomy, learning surgical procedures by practicing on dummies, development of sophisticated surgical instruments and the art of plastic surgery constitute the hallmark of classical Ayurvedic surgery. Sushruta, the Ayurvedic surgeon of yore is revered today as the father of surgery.​

Department of Shalakya Tantra (ENT, Dentistry and Ophthalmology)

Imparts training in areas of specialization like ENT, Ophthalmology, Dentistry and diseases of the head.  Special training is given on management of certain eye diseases, conditions like sinusitis, migraine and such other conditions for which Ayurvedic treatment is effective. It was in the field of Ayurveda that the specializations of ENT, Ophthalmology and Dentistry first developed. Traditions of Ayurvedic ophthalmology still survive in Kerala. Traditional experts in this field successfully manage many diseases that affect the eye like diabetic retinopathy, glaucoma, macular degeneration and the like. Classical texts of Ayurveda describe a surgical procedure for the management of cataract.

Department of Stri Roga and Prasuti Tantra (Gynaecology, Obstetrics )

Imparts training in Ayurvedic Gynaecology, Obstetrics and Paediatrics. Gynaecology deals with menstrual disorders, diseases of the female genital tract and veneral diseases. Ayurveda advises a special regimen for care of the pregnant woman. It also lays down certain guidelines to ensure the birth of a healthy child. Obstetrics deals with conditions related to maternity as well as normal and abnormal delivery.

Department of Dravyaguna (Ayurvedic Pharmacology)

Deals with principles of Ayurvedic pharmacognosy and pharmacology with a special focus on identification of controversial drugs, adulterants and substitutes used in Ayurvedic practice. Ayurveda has developed a unique approach to understanding pharmacology of natural substances through meticulous analysis of taste, physico-chemical properties, potency and bio-transformation of the drug. Ayurveda traces the pathway of drug action right from the point of its ingestion through various stages of its digestion and metabolism to the point of its excretion from the body.  Ayurveda understands drug action as the net result what happens when the drug acts on the body and the body acts on the drug. Dravyaguna deals knowledge of nomenclature (namajnana), pharmacognosy (rupajnana), pharmacology (gunajnana) and pharmacotherapeutics (yuktijnana). The hallmark of Ayurvedic pharmacology is its theoretical framework that attempts to understand complex interactions between various ingredients in a formulation that work in synergestic manner to produce a pharmacotherapeutic action that initiates the process of healing.

Kaumarabhritya (Paediatrics)

Ayurveda offers special treatment modalities for post natal care of the mother. Paediatrics deals with care of the new born as well as diseases affecting children. Traditions of Ayurvedic paediatrics are still alive in India. In ancient times, Ayurvedic paediatrics was a separate school of medicine, although it was not as prominent as the schools of medicine and surgery. The Kashyapa Samhita is a classical text on Paediatrics which has been preserved in a mutilated form and is more than 2000 years old.

Department of Swastha Vrittam (Social and Preventative Medicine)

Imparts training on the principles and practice of Social and Preventative Medicine at both the personal and communal levels. Promotion of positive health is dealt with from the Ayurvedic viewpoint. Naturopathy and Yoga also come under the purview of this department. Social and Preventative Medicine in Ayurveda deals with elaborate guidelines and regimens for maintaining and promoting health of the individual and the community as a whole. Regulation of life style, diet and behaviour on the basis of diurnal, seasonal and geographical variations as well as the constitution of the individual is an important component of preventive medicine in Ayurveda. Ayurvedic dietetics is a discipline in itself. Measures for periodical purification and rejuvenation of the body aims to promote vitality and positive health of the person. Ayurveda also deals with the principles of epidemiology and the prevention and management of communicable diseases. This department gives comprehensive training on preventive aspects of health care integrating modern concepts with principles of Ayurveda as well as yoga and naturopathy.

Department of Maulika Siddhanta (Basic Principles of Ayurveda)

This department deals with the teaching of subjects that are foundational for the study of Ayurveda like Sanskrit, basic principles, classical Ayurvedic texts, history of Ayurveda and epistemology. Proficiency in Sanskrit is indispensible to properly understand the import of classical Ayurvedic writings. This has to be further substantiated by a thorough grounding in the classical knowledge systems of India including both the theistic and atheistic schools.  The evolutionary history of Ayurveda spans a few thousands of years and provides interesting insights into the devlopment of the world of medicine itself. It is also essential for the aspirant of Ayurveda to become well versed with the approach of knowledge building delineated in the classical texts of Ayurveda, which accomodates but transcends the methods of science. The department of basic principles prepares the students with the basic intellectual tools necessary to engage in a serious study of Ayurveda.

Department of Rasashastra and Bhaishajya Kalpana (Medicinal Chemistry and Pharmacy)

With the help of well equipped labs, this department imparts training in medicinal chemistry and preparation of highly potent medicines from minerals and metals. It also deals with the principles and practice of Ayurvedic Pharmacy with its varied pharamaceutical methods and dosage forms. Knowledge of Ayurvedic Pharmacy encompasses field identification of medicinal plants and other natural substances, collection and storage procedures of raw materials, preliminary processing of raw drugs, elaborate and sophisticated methods of pharmaceutical processing and preservation of prepared medicines.  Pharmacy in Ayurveda essentially involves extraction of essential principles from the natural world in aqueous, fatty or alcoholic medium through a systematic process of cooking and their conversion into suitable dosage forms. In keeping with tradition, this department gives shape to the Ayurvedic physician who does not merely prescribe finished medicines, but is also capable of formulating and preparing medicines according to the specific needs of a patient.

Department of Rachana Shareeram (Anatomy)

The department of anatomy provides rigorous training in dissecting cadavers and critically examines both ancient and modern views on anatomy. The surgical school of Ayurveda pioneered the technique of treating dead bodies in flowing water and exposing the underlying structures by scraping the skin using soft instruments to gain accurate knowledge of minute structures that make up the human body. This practice declined over the ages due to various factors and today Ayurvedic Anatomy needs to be supplemented with modern knowledge. A unique aspect of Rachana Shareeram in Ayurveda is the knowledge of the vital points or marmas, which have to be protected when performing surgical procedures and injury to which can lead to disastrous consequences including death. Knowledge of these vital points and techniques to manipulate them is essential to become proficient in therapeutic massage that stimulates prana and revitalises the body.

Department of Roga Vijnana (Pathology)

This department deals with nosology (classification of diseases) and techniques of diagnosis. Training is given in both ancient methods of diagnosis and relevant modern investigations. Ayurveda lays great stress on detecting diseases in the very early stages of development and has developed an elaborate system of subtle diagnostic techniques to identify imbalances in the body before they transform into complicated disease processes. Ayurveda gives equal emphasis on understanding origins of disease, the disease process and the external manifestations. It understands disease as a paradoxical combination of failure of physiological mechanisms and attempts by the body to restore normalcy.  Diagnosis involves a clear understanding of the therapeutic response that has been initiated by the body based on which an appropriate treatment strategy is visualised. An inherent strength of Ayurveda is its emphasis on strengthening the body from within to reverse the disease process. Roga vijnana involves developing subtle skills of pulse diagnosis and other subjective methods to feel and understand the subtle interactions between the body and mind in health and disease.

Department of Kriya Shareeram (Physiology)

Deals with the study of normal physiology in human beings from both ancient and modern viewpoints with sufficient practical training. The corner stone of Ayurvedic physiology is the dosha-dhatu-mala siddhanta. This theory provides a holistic framework to understand how the body digests and metabolises food into subtle forms of matter and energy to create and maintain a delicately balanced internal environment that is conducive to the preservation of the life process.  The doshas represent the dynamic balance of opposing factors that govern the physiological processes in the body while the dhatus represent the structural components of the body and the malas the wastes that are thrown out of the body or recycled to support the structure or functions of the body. This department trains the student in basic concepts of Ayurvedic physiology as well as the essential aspects of modern physiology comparing and contrasting the convergence and divergence of ancient and modern viewpoints.

Department of Agada Tantra and Vyavaharayurveda (Toxicology, Jurisprudence and Forensic Medicine)

Imparts training in toxicology, jurisprudence and forensic medicine, which explores the causes of unnatural behaviour and death. Ayurveda has nurtured and sustained a sophisticated system of toxicology that combats the effects of natural poisons posing long term or immediate threat to the continuity of the life process. This branch was so well developed in ancient India that the physicians of those days won the admiration of Alexander the Great, whose soldiers were miraculously cured of snake bites by native poison healers. Experts in Ayurvedic toxicology and snake poison healing have survived into modern times. Systematic clinical research in this branch can help in understanding the scope and  potential of the Ayurvedic approach of healing in management of emergency conditions. Another important aspect of Ayurvedic toxicology is the treatment of chronic poisoning. Legal aspects of medicine, which are discussed in works like Arthashastra of Kautilya need to be intergrated with modern concepts and techniques of Forensic medicine. This department equips the student to become well versed in understanding natural and unnatural modes of death as well as medico-legal aspects of medical practice.

Department of Panchakarma

Deals with the Purification therapies of Ayurveda and provides a basic understanding of the principles of Shodhana. Panchakarma includes Vamana, Virechana, Nasya, Basti karma & Raktha Mokshan, using a varied kinds of Ayurvedic medicines. As far as the treatment methods are concerned Ayurveda has described the use of Shamana (Palliative treatment) and Shodhana (Bio-Purifaction methods - Panchakarma) methods. Panchakarma literally means five methods of body purification. These methods are employed in the healthy to prevent diseases and to improve the immunity as also in the sick to treat a number of diseases.  Recognizing that many illnesses result from the build-up of toxins in the body that impair the functioning of its natural defenses: the lymph, circulatory and immune systems, Panchakarma promotes healing and restoration by eliminating these toxins from the body. Unlike other detoxification programs, Panchakarma is a gentle process that achieves deep cleansing without discomfort and allows rejuvenating energy to flow freely through the body.