At the beginning of the 20th century the old archives of Leiden University were transferred from the Academy Building to the University Library: first the archives of the Senate and of the Board of Governors; some years later those of the Faculties followed. In the 1930s finding aids of these archives (running up to 1877) were compiled in the State Archives in The Hague. In later years various other archives and documentation created by Leiden University were transferred to the University Library. Their contents were listed and described in 2000-2001 by the Centrale Archief Selectiedienst (Central Archives Selection Service), Winchoten. Below is an overview of all University archives.

• Archives of the Governors – Executive Board – University Council
  — Archives of the Governors, 1574-1815, 1815-1877, 1878-1953
  — Archives of the Governors – Board of Directors, 1952-1989
  — Documents regarding events during the Nazi-occupation in World War II, 1940-1951 and 1971
  — Matriculation registers of the students, 1877-1977 (1987)
  — Archives of the University Council, (1967) 1971-1989
• Archives of the Senate — Board of Deans — Rector
  — Archives of the Senate and Faculties, 1575-1877
  — Archives of the Rector and the Senate, 1875-1972
  — Archives of the Board of Deans and the Rector, 1971-1989
• Archives of the Faculties: 
  — Archives of the Senate and the Faculties, 1575-1877
  — Archives of the Faculty of Theology, 1815-1968
  — Archives of the Faculty of Law, (1773-)  1850-1979
  — Archives of the Faculty of Arts & Philosophy, 1856-1952
  — Archives of the Faculty of Arts, 1948-1984
  — Archives of the United Faculties of Law and Arts & Philosophy, 1883-1958
  — Archives of the Faculty of Medicine, 1847-1958 (1965)
  — Archives of the Laboratory of Medical Chemistry, 1926-1955
  — Archives of the Faculty of Mathematics & Physics, (1835-), 1899-1955
  — Archives of the Zootomical (later Zoological) Laboratory, 1868-1954 and of C.J. van der Klaauw, professor of zoology, 1934-1959
• Archives of Leiden University Library, 1595-1869 (-1974)
• Archives of institutes connected with Leiden University, 1828-1994

The online catalogue contains links to collection guides for all University archives, with detailed (electronic) inventories with the possibility to directly request items for consultation in the Special Collections Reading Room.

Since 1909, 25 inventories of the Leiden University archives have been published. See for bibliographical data: Catalogues of the Holdings of Leiden University Libraries, section Q. The digitized finding aids in the Collection guides (see above) contain the same data and are now the most important point of entrance.