Vaisesika theory of absence draws a type of distinction between simple absence (atyantabhava) and difference (anyonyabhava). Difference is the absence of a relation of identity between two things. Absence in Vaisheshika philosophy is not similar to the concept of non-existence. Vaisesika theory of absence states that it would be an absurdity to go in search of Hamlet in order to find out whether he really exists or not - his non-existence is not a merely contingent lack in the world of things. The absence of water on the moon, on the other hand, is a contingent and concrete fact; so too is the absence of colour in a person`s cheeks. For it is often the case that the absence of something somewhere is more salient than any fact about what is present there.

There is one relatively straightforward way to interpret the idea of absence. As per Vaisheshika philosophy, absences are things of a different type from any presence. Further, for various reasons, the Vaisesika theory does not consider this to be an adequate explanation of the category. One problem is that it makes absences more like relations as compared to things, and this does not keep to the spirit of the Vaisesika idea that absences are entities. In fact, absences do display much relation-like behaviour. The view of the early thinkers is that the absence of an absence is nothing but a presence; it is not admitted as a new absence for there would then be an infinite regress. According to the new school, however, the absence of an absence is a distinct absence, and there is no regress as the third absence is identical to the first. Further, as per the Vaisesika theory, absence is considered as a classical proposition and so, in particular, that an absence of an absence is identical to an absence. A double contradiction, however, is defined on inherence edges followed by a negation defined on absent qualifier edges and for that reason behaves non-classically.

The relation between an absence and its location is clearly not the same as the relation between a presence and its location. For it is clear that, when a person is absent from a room, his absence is not in the room in the same sense that the other things in the room are.