The fifth century BC is one of the most brilliant of Greek history. Pericles, as the leader of a splendid Athens, promoted the entry into his polis of the new scientific movement that until then had developed primarily in Ionia and in the Italian peninsula. However, their research raised suspicions among the Athenians, who regarded it as a risk for traditional religion. In spite of the somewhat flexible and plural character of the Greek religion, in this period three famous trials took place in which different philosophers were tried for impiety: Anaxagoras, Protagoras and Socrates. The controversy between religion and philosophy can lead us to an oversimplification of the facts. Thus, several modern scholars have understood philosophy as an exorcism of myth and therefore as something necessarily guiding to a progressive elimination of the divine from the worldview. We intend to interpret this conflict only as a change in understanding of the divinity, rather than a suppression of it. This has, of course, effects on religion, but it does not drag inevitably to irreligion.