The notion of an individual and the related issues on individuation are topics that appear in the philosophical discussion ever since the antiquity. The idea of an individual thing is intuitively clear: an individual is something of a specific kind that is a unity, having its own identity, and being so that it is possible at least in principle to discern it from any other individual, even of similar species. But when we try to leave the intuitive realm and push this idea to a logical analysis, we find a cluster of problems that are difficult to overcome within standard logico-mathematical contexts. In this work, we shall be concerned with some aspects of this intuitive concept of an individual and on some related facts about individuation taken from recent discussions that arose ever since the inception of quantum theory, pushing the discussion to a “logical” view, which in our opinion is still lacking in the usual debates on such issues. In the final part of the paper, we propose a metaphysics where the notion of identity is substituted, for some objects, by a weaker notion of indiscernibility, and we try to justify such a move. In most of the uses of the expression “quantum theory”, we shall not make explicit the distinction between the non-relativistic and the relativistic approaches, although they of course are quite different, for we think that the problems as we shall present them appear in both versions. But, as the text goes, the context will distinguish between them and these questions will become clear to the reader.