The Vaiśeṣika school is known for its insights in naturalism. It is a form of atomism in natural philosophy.[6] It postulated that all objects in the physical universe are reducible to paramāṇu (atoms), and one's experiences are derived from the interplay of substance (a function of atoms, their number and their spatial arrangements), quality, activity, commonness, particularity and inherence. Everything was composed of atoms, qualities emerged from aggregates of atoms, but the aggregation and nature of these atoms was predetermined by cosmic forces. Ājīvika metaphysics included a theory of atoms which was later adapted in the Vaiśeṣika school

• Pratyakṣa (प्रत्यक्ष) means perception
  • Internal
    • inner sense, the mind
      • requirements for internal perception
        • pratibha (intuition),
        • samanyalaksanapratyaksa (a form of induction from perceived specifics to a universal),
        • jnanalaksanapratyaksa (a form of perception of prior processes and previous states of a 'topic of study' by observing its current state)
  • External
    • arising from the interaction of five senses and worldly objects
      • requirements for Correct Perception
        • Indriyarthasannikarsa (direct experience by one's sensory organ(s) with the object, whatever is being studied),
        • Avyapadesya ( according to ancient Indian scholars, where one's sensory organ relies on accepting or rejecting someone else's perception),
        • Avyabhicara (does not wander; correct perception does not change, nor is it the result of deception because one's sensory organ or means of observation is drifting, defective, suspect)
        • Vyavasayatmaka (definite; correct perception excludes judgments of doubt, either because of one's failure to observe all the details, or because one is mixing inference with observation and observing what one wants to observe, or not observing what one does not want to observe)

• Anuman ( inference )
  • pratijna (hypothesis),
    • sadhya (that idea which needs to proven or disproven)
    • paksha (the object on which the sadhya is predicated).
      • The inference is conditionally true if sapaksha (positive examples as evidence) are present,
      • if vipaksha (negative examples as counter-evidence) are absent.
  • hetu (a reason),
  • and drshtanta (examples).
    • Observing smoke and inferring fire is an example of Anumana.
  • A conditionally proven hypothesis is called a nigamana (conclusion)

According to the Vaisheshika school, all things that exist, that can be cognized and named are padārthas (literal meaning: the meaning of a word), the objects of experience. All objects of experience can be classified into six categories, dravya (substance), guṇa (quality), karma (activity), sāmānya (generality), viśeṣa (particularity) and samavāya (inherence). Later Vaiśeṣikas (Śrīdhara and Udayana and Śivāditya) added one more category abhava (non-existence). The first three categories are defined as artha (which can perceived) and they have real objective existence. The last three categories are defined as budhyapekṣam (product of intellectual discrimination) and they are logical categories.

• Dravya (substance): There are nine substances. They are, pṛthvī (earth), ap (water), tejas (fire), vāyu (air), ākaśa (ether), kāla (time), dik (space), ātman (self or soul) and manas (mind). The first five are called bhūtas, the substances having some specific qualities so that they could be perceived by one or the other external senses.
• Guṇa (quality): The Vaiśeṣika Sūtra mentions 17 guṇas (qualities), to which Praśastapāda added another 7. While a substance is capable of existing independently by itself, a guṇa (quality) cannot exist so. The original 17 guṇas (qualities) are, rūpa (colour), rasa (taste), gandha (smell), sparśa (touch), saṁkhyā (number), parimāṇa (size/dimension/quantity), pṛthaktva (individuality), saṁyoga (conjunction/accompaniments), vibhāga (disjunction), paratva (priority), aparatva (posteriority), buddhi (knowledge), sukha (pleasure), duḥkha (pain), icchā (desire), dveṣa (aversion) and prayatna (effort). To these Praśastapāda added gurutva (heaviness), dravatva (fluidity), sneha (viscosity), dharma (merit), adharma (demerit), śabda (sound) and saṁskāra (faculty).
• Karma (activity): The karmas (activities) like guṇas (qualities) have no separate existence, they belong to the substances. But while a quality is a permanent feature of a substance, an activity is a transient one. Ākāśa (ether), kāla (time), dik (space) and ātman (self), though substances, are devoid of karma (activity).
• Sāmānya (generality): Since there are plurality of substances, there will be relations among them. When a property is found common to many substances, it is called sāmānya.
• Viśeṣa (particularity): By means of viśeṣa, we are able to perceive substances as different from one another. As the ultimate atoms are innumerable so are the viśeṣas.
• Samavāya (inherence): Kaṇāda defined samavāya as the relation between the cause and the effect. Praśastapāda defined it as the relationship existing between the substances that are inseparable, standing to one another in the relation of the container and the contained. The relation of samavāya is not perceivable but only inferable from the inseparable connection of the substances.
• Abhava (non-existence)