There are two fundamental questions concerning the choice and presence of objects in various formal systems: (1) Where do these objects come from? (2) What do (can) we know about them? To answer these questions I introduce the notion of a proto-ontology as the pre-theoretic realm of (unspecified) entities from which the basic objects – individuals – of the formal system S are postulated. The pragmatic aspects of such choices are investigated with regard to first-order logic, both pure and applied, set theory and mereology. It is claimed that the postulated (chosen, constructed) objects enter the formal system S with a package of properties and relationships, the recognition of which depends on the interpretation and application of the available predicates of S. If these properties and relationships are not made explicit, a possible clash may arise between them and the properties and relationships “assigned” to the individuals of S by the interpreted predicates of S. As regards the relationship between logic and metaphysics, I contend that logic can perhaps be viewed as the articulation of the fundamental features of proto-ontological objects without which no discourse or theory would be possible. In this sense logic could also be viewed as a theory and method of the construction of a well-articulated metaphysical theory.