This study aims to examine the relations of influence and tension between the so-called natural philosophy and the metaphysics between the Renaissance and Modernity. Therefore, anatomy was taken as a case study. More specifically, the works of three anatomists were chosen. They are: Andreas Vesalius (1514- 1564) and his De humani corporis fabrica libri septem (1543); William Harvey (1578-1657) and the Exercitatio anatomica de motu cordis et sanguinis in animalibus (1628); and Nicolas Steno (1638-1686) and his Discours sur l anatomie du cerveau (1669). Vesalius was selected as a representative of Renaissance thought, Harvey is located in the transition to Modernity, while Steno is eminently a modern. Moreover, some of the philosophical and scientific contexts in which the three lived were also addressed, so the philosophies of Aristotle, Galen, Paracelsus, Francisco Sanches, Descartes, Hobbes and Spinoza were partially studied. Emphasis is given to the transition from a vitalist medical scientific thought to a mechanistic one. In comparing the works of the three anatomists, differences and similarities were observed and Skepticism eventually emerged as a protagonist.