Bayle was a notable advocate of religious toleration, and his skeptical philosophy had a significant influence on the subsequent growth and development of the European Age of Enlightenment.

Just before that event, Bayle had fled to the Dutch Republic, where he almost immediately was appointed professor of philosophy and history at the École Illustre in Rotterdam.

At Rotterdam, Bayle published his famous Reflections on the Comet [fr] in 1682, as well as his critique of Louis Maimbourg's work on the history of Calvinism.

The reputation achieved by this critique stirred the envy of Pierre Jurieu, Bayle's Calvinist colleague of both Sedan and Rotterdam, who had written a book on the same subject.

After losing his chair, Bayle engaged in the preparation of his massive Dictionnaire Historique et Critique (Historical and Critical Dictionary), which effectively constituted one of the first encyclopaedias (before the term had come into wide circulation) of ideas and their originators.

The English translation of The Dictionary, by Bayle's fellow Huguenot exile Pierre des Maizeaux, was identified by American President Thomas Jefferson to be among the one hundred foundational texts to form the first collection of the Library of Congress.

Bayle rejected the use of scripture to justify coercion and violence: "One must transcribe almost the whole New Testament to collect all the Proofs it affords us of that Gentleness and Long-suffering, which constitute the distinguishing and essential Character of the Gospel."

"[5]Richard Popkin has advanced the view that Pierre Bayle was a skeptic who used the Historical and Critical Dictionary to criticise all prior known theories and philosophies.

Bayle was critical of many influential rationalists, such as René Descartes, Baruch Spinoza, Nicolas Malebranche and Gottfried Wilhelm Leibniz, as well as empiricists such as Thomas Hobbes, John Locke, and Isaac Newton.