According to the Siddha concepts, there are two dominant entities, namely matter and energy, which have a great influence in shaping the nature of the universe. They are called Siva and Sakthi in the Siddha system. Matter cannot exist without energy and vice versa. Thus, both are inseparable. The concept of five proto-elements and three gunas in this system of medicine is quite similar to the Ayurvedic concept pertaining to them. This system also believes in the role of the three humors, namely vatta, pitta and kapha. According to this system, all objects in the universe are made up of five basic elements—earth, space, water, fire and air.

The diagnosis or identification of causative factors of diseases in the Siddha system is carried out by the well-known ashtasthana pareeksha (examination of eight sites), which encompasses examination of nadi (pulse), kan (eyes), swara (voice), sparisam (touch), varna (color), na (tongue), mala (faeces) and neer (urine). These examination procedures are provided in greater detail in classical Siddha literature.