A close examination of the literature on ontology may strike one with roughly two distinct senses of this word. According to the first of them, which we shall call traditional ontology, ontology is characterized as the a priori study of various “ontological categories”. In a second sense, which may be called naturalized ontology, ontology relies on our best scientific theories and from them it tries to derive the ultimate furniture of the world. From a methodological point of view these two senses of ontology are very far away. Here, we discuss a possible relationship between these senses and argue that they may be made compatible and complement each other. We also examine how logic, understood as a linguistic device dealing with the conceptual framework of a theory and its basic inference patterns must be taken into account in this kind of study. The idea guiding our proposal may be put as follows: naturalized ontology checks for the applicability of the ontological categories proposed by traditional ontology and give substantial feedback for it. The adequate expression of some of the resulting ontological frameworks may require a different logic. We conclude with a discussion of the case of orthodox quantum mechanics, arguing that this theory exemplifies the kind of relationship between the two senses of ontology. We also argue that the view proposed here may throw some light in ontological questions concerning this theory.