During the latter decades of the sixteenth century, most of the institutional libraries then existing in the Netherlands, i.e. those of monasteries and other ecclesiastical institutions, were dispersed. At the same time, the first town libraries were established in, for example, Amsterdam (1578), Utrecht (1581), Gouda (1590), Haarlem (1596) and Deventer (1597) and other towns followed. The collections were often taken from former local monastic libraries. A number of town and church libraries (often difficult to distinguish) had already been established before the Reformation and often owed their origin to the spirit of the early sixteenth-century grammar school with its mixture of Roman Catholic piety and Erasmian humanism rather than to the Reformation. The best-known example is the Zutphen Librije: established in 1562 and still in its original accommodation with much of the original furnishing retained. Comparable church libraries still in existence are those of Edam (1575; books now on loan to the Koninklijke Bibliotheek, The Hague) and Enkhuizen (1590). The older 'librijes' and the younger town libraries shared the same fate in the following centuries: prosperous times under the authority of a minister, headmaster or mayor with a love of books, alternating with periods of gross neglect. Catalogues were published in the better periods; the oldest example is the catalogue of the town library of Utrecht (1608). Amsterdam, Haarlem, Enkhuizen and other towns followed later in the seventeenth century.

In 1575, the first university in the still-young Republic was founded in Leiden, followed by Franeker (1585), Groningen (1614), Utrecht (1636) and Harderwijk (1648). These universities all had libraries from the very beginning except Utrecht where the existing town library was used for that purpose (only in 1816 was it granted the status of university library). From time to time, most of these university libraries had catalogues printed. The Leiden catalogue of 1595 is the earliest catalogue ever published of an institutional library. These libraries were all small and limited in the subject fields covered, not only when compared to modern standards, but also in comparison to many private libraries of the time. Not much was to change in the following century. They were, partly because of this, of lesser importance to scholars and men of letters. In 1653, the Leiden lawyer Johannes Thysius, who died at an early age, left his sizeable library 'for the good of the public'. The legacy also included funds for the construction of suitable accommodation and for the expansion of the collection. In 1655, a fine library building was opened on the Rapenburg in the Dutch Classicist style and, because not many new books were acquired, the Bibliotheca Thysiana is still a unique example of a seventeenth-century scholarly library.

The Dutch library landscape of small and often neglected university and town libraries overshadowed by large and rich private collections and without a national library such as, for example, the Bibliothèque du Roi in France, would only be enriched in the second half of the eighteenth century by the establishment of commercial lending libraries, reading circles and social or cultural societies.