Inspired by the English-speaking tradition of advanced studies institutes, there were originally four Cini Foundation institutes, founded in the 1950s: Art History (1954), History of the Venetian State and Society (1955), Literature, Music and Drama (1957), and Venice and the East (1958).

Created to study all aspects of the history of Venetian culture, the institutes have provided opportunities and resources for specialists and scholars by promoting initiatives and research projects, at times in collaboration with major international cultural institutions.

In 1978 the Italian Antonio Vivaldi Institute became part of the Cini Foundation.

In 1985 a separate Institute of Music was formed to be independent of the Institute of Literature.

In 1999 the Intercultural Institute for Comparative Music Studies also formally joined the Foundation. In 2002 the Venice and Europe Institute was given an independent status, after previously having been a section of the Institute for Venice and the East.

Founded in 2003, the Research Center for the Documentary Sources of European Musical Life aims to develop a number of aspects of research already being pursued in the Institute of Music.

In 2007, the Study Center for Documentary Research into European Theatre and Opera was also created.

In addition to the regular publication of periodicals, each Institute or Center organizes and promotes exhibitions, conferences and workshops in the field of its own research activities.