The third-largest in France, the Mazarine Library's incunabula collection mainly derives from Cardinal Mazarin's private library, revolutionary confiscations and several exchanges with the royal (and later national) library. In the first collection put together for Mazarin by Gabriel Naudé figured a copy of the Latin Bible printed by Johann Gutenberg in Mainz about 1455. In 1652, during the Fronde, the volume briefly passed into the hands of Jean Jobert, a lawyer in the Parlement de Paris, who gave it back to Mazarin when he returned to power in 1654. This 42-line Bible was then not yet identified as the first printed book in the history of mankind; it did not acquire that reputation until the eighteenth century with Guillaume-François Debure's bibliographic appraisal about 1762, based precisely on the copy in the Mazarine Library. In 1668, in the course of an exchange on Colbert's initiative, about 150 incunabula were taken from the Mazarine Library and sent to the royal library. They are now in the rare book room of the French National Library. But, in return, the Mazarine acquired incunabula from the collection of the Aragonese kings of Naples, Francis I or his mother, Louise of Savoy. The revolutionary confiscations later added some remarkable sets of printed books from the fifteenth century, taken this time from ecclesiastical libraries in Paris (College of the Sorbonne, the abbeys of Saint Victor and Saint Germain des Prés) or Belgium (Carmelites in Mechelen, Dominicans in Bois le Duc).

Italian books make up a large part the collection: 40% of the editions were printed in Italy and 75 editions are in Italian. The collection is encyclopaedic in scope, but particularly strong in history, ecclesiastic scholarship, geography and the sciences; there are, however, few books of hours compared with collections of comparable size. Among the rarest editions are a few vernacular works in French, Italian or Flemish, in particular a fine set of Gothic leaflets printed in Paris in the 1490s, or the only surviving copy of the first edition of the Shepherds' Calendar (1491), from the library of Notre Dame Cathedral in Paris. Among the finest illuminated books in the collection is a copy of Lancelot of the Lake published by Antoine Vérard in 1494 and decorated in Paris at the turn of the fifteenth and sixteenth centuries, and the Epigrams of Martial, in the editio princeps printed in Rome about 1470, and painted by the anonymous Master of the Putti.

An inventory of the Library's incunabula was published in 1986; they are now listed in SUDOC and the Incunabula Short Title Catalogue. The Mazarine is taking part in the CR2I project to develop regional computer catalogues of the incunabula. Lastly a selection of 250 incunabula (unica and remarkable copies) are available in the Institut de France Digital Libraries with the help of the Digital Scientific Library.