Until the annexation in March 1938, Vienna had various decentralized medical libraries set up in the first half of the nineteenth century (Second Medical School) to keep pace with the rapid development of the individual medical disciplines. These libraries were located in Viennese hospitals, as clinic and institute libraries in the Medical Faculty of the University of Vienna, and in the General Hospital. There were also non-university research and professional organizations and interest groups, mostly in the form of associations. The Medical Faculty in Vienna was subject to massive changes following the annexation, with a huge wave of dismissals and persecution of academic staff and students. This caesura had grave consequences on the development of the libraries. Decades of uninterrupted library work came to an abrupt end in March 1938. Existing research networks were completely destroyed. Long-standing libraries were closed, including the Medical Reading Room at the General Hospital in October 1939, which until then had been one of the largest hospital libraries in Vienna. The reform and reorganization by the Nazi regime also had serious consequences for the libraries of non-university institutes. Before the annexation, there were over sixty medical associations, research, professional and interest groups, which were now "aligned" within the Nazi power structures or closed down and their assets expropriated or transferred to the replacement Nazi institutions. Many books ended up in the following years in the antiques market. They included the library of the Doctoren-Kollegium, which was transferred in 1939 to the Reichsärztekammer in Vienna and only in 1970 handed back to the library of the Institute of the History of Medicine. The first to be affected by the closure of medical libraries, however, were Jewish associations, such as that of the Akademischer Verein jüdischer Mediziner – a branch of the Medical Section of the Gesamtverband jüdischer Hochschüler Judäa. By the end of 1939 the medical associations in Vienna had practically disappeared.

It was not until the 1970s that a major reorganization of inventories of medical libraries was undertaken, one that continues to have repercussions today. Under the 1975 University Organization Act, all clinic and institute libraries were put in the charge of the University of Vienna Library. In 1986 a library was opened in the Medical Faculty of the University of Vienna and all of the works from the decentralized clinics and medical institutes incorporated in it. After this Faculty Library opened in 1989 at the site of the new General Hospital (university clinics), all of the hitherto independent clinic and institutes were subsumed in it until 1994, when the Austrian Central Library for Medicine was established. This involved the transfer of the historical contents to the present-day University Library and the Zweigbibliothek für Geschichte der Medizin (Branch Library for the History of Medicine). It included the Obersteiner library and the historical contents of the Bibliothek der Gesellschaft der Ärzte in Wien (Library of the College of Physicians in Vienna), which were loaned to it in three phases in 1960s, 1976 and 2003. Through the acquisition of other special collections, most of the medical history works were now combined in one central location, forming a special library, whose heterogeneous and unsystematically arranged contents are today the unofficial archive library of medical history in Austria. When the Medical Faculty of the University of Vienna became the stand-alone Medical University of Vienna in 2004, the former Austrian Central Library of Medicine became the new university's library. It currently contains around 780,000 monographs and magazines and is the largest medical library in Austria.

The provenance research carried out at the University Library of the Medical University of Vienna since 2007 has to take account of the numerous interruptions in the development and history of the individual libraries and collections. In that context, mention should be made of the absence – except for the former Institute for the History of Medicine and the Bibliothek der Gesellschaft der Ärzte in Wien – of inventory lists and the patchy if not completely missing documentation of the library administration and acquisitions policy. The universities that became autonomous in 2004 were under no legal obligation to investigate their contents in accordance with the 1998 Art Restitution Act (amended in 2009). The rectorates of the Medical University of Vienna fully supported such research in its library. In accordance with the recommendations, the following restitutions have been made: Alfred Arnstein (2012), Stefan Auspitz (2018), Bibliothek Sassenbach (2011), Raoul Fernand Jellinek-Mercedes (2012), Hans Peter Kraus (2014), Carl Julius Rothberger (2010), and Philip Suschitzky and Adele Suschitzky (2014). Restitution recommendations also exist for three further dossiers: Alois Fantl, Richard Löwi, and Maximilian Weinberger. Provenance research at the University Library of the Medical University of Vienna continues.