Among the Library’s special collections, the one most intimately linked to the history of the University is with no doubt the Doctoral Thesis Fund. The collection consists of about 20,000 dissertations from numerous Italian and foreign academic institutions, many of which are Jesuit. However, the Fund finds its gravitational centre in the approximately 7,000 theses defended at the Pontifical Gregorian University since 1934, therefore from the dawn of the University’s  refoundation in the Piazza della Pilotta headquarters. The Library, which also houses the ancient card catalogue by author and by subject, receives in duplicate copies from the Registrar’s Office all papers submitted by students, whether they are full versions or extracts. While second copies are kept in the Book Tower, first copies are bound together by Faculty and placed on open-shelf in a dedicated room, accessible from the first walkway of the historical reading room. Precious testimony of university research carried out in almost a century, the Fund lends itself to multiple lines of investigation; moreover, it also holds some "relics" of great interest, such as the works of famous alumni of the Pontifical Gregorian University.

The Hagiographic Fund preserved by the Library currently consists of about 2,000 documents issued by the Congregation for the Causes of Saints, the Vatican Ministry that oversees the canonical procedure for the causes of beatification and canonization. The Apostolic Constitution Divinus Perfectionis Magister, promulgated by John Paul II on January 25th, 1983, and the respective Normae servandae in inquisitionibus ab Episcopis faciendis in causis sanctorum of February 7th, 1983, in addition to having reformed the procedure of canonization causes, have given a new structure to the Congregation, that has been endowed with a College of Supervisors with the task of taking care of the preparation of the Positiones super martyrio or super vita, virtutibus et fame sanctitatis of the Servants of God. The Positio is a document (or a collection of documents) used in the canonical process and collects the results of the diocesan inquiry, which is submitted to the attention of the Congregation. For decades, the Library has regularly received the emanations of the Congregation for the Causes of Saints, establishing the rich Hagiographic Fund preserved on the first walkway of the Distribution Room. The documents held are only partially catalogued, and the very nature of the collection, with its strong in progress connotation, requires a particular bibliographic treatment, which will be the focus of a future project.

The most consistent of the Library’s special collections is also the one that has the most interesting history, as it is of great interest the history of its founder: the collection is the Wetter Fund and its founder is the Austrian Jesuit Gustav Andreas Wetter. Born in Vienna in 1911, in 1930 he entered the Russicum Institute and began his studies at the Pontifical Gregorian University. In 1943 he obtained the chair of Russian philosophy at the Oriental Institute directing his research on the development of Marxism-Leninism in Russia and on the main Marxist philosophers. In 1944, he gave a series of lectures on Materialism and was soon acknowledged as one of the most authoritative Western thinkers on the subject. In 1948 the first edition of his Der dialektische Materialismus, seine Geschichte und sein System in der Sowjetunion was put into print, published in Italian by Giulio Einaudi, a notoriously leftist editor, under the title Il Materialismo dialettico sovietico. His work spread internationally and consecrated him not only in the religious academic world, but also in the secular world, often indifferent or hostile to Jewish-Christian values. His studies and his many international contacts gave him the opportunity to set up a world-class library at the Russicum dedicated to Marxism. The relocation to the Pontifical Gregorian University, where he had already taught since 1954, created the conditions for the foundation, in 1970, of the Centre for Marxist Studies, to which the precious book collection was linked. During the following years the collection was further enriched up until the death of its founder in 1991, reaching the remarkable amount of 42,000 volumes. What today is - of course - called the Wetter Fund, is a large and organic core of works concerning Marxism, especially Marxist philosophy, Bolshevism, Soviet and international Communism, and contemporary atheism. It is undeniable that this Fund, due to its history and its location in the Gregorian Library, therefore in the heart of the papal Rome, represents a truly unique reality that probably derives from an unrepeatable experience.

The Fund of the Social Sciences Seminary is what survives from the long tradition of book collections established within the individual Academic Units of the Pontifical Gregorian University and kept separate from the Library's documentary collection for decades. These thematic libraries, which increased with works more directly related to teaching on the impulse of professors, were usually located in classrooms adjacent to the deanery, spaces that served as classrooms for teaching and study. Then the volumes periodically passed into the Library, to make way for the most recent and more related to current use publications. The Seminaries remained fundamental spaces for students at least until the expansion of the Library in the early 1980s, with the annexation of the large Room V. At the concentration of students followed the concentration of the book collections belonging to the Seminaries, which were gradually incorporated into the Library's collection, all except the one linked to the Seminary of Social Sciences. The Fund arose from the great expansion of sociological studies in universities starting from the 1950s and 1960s; in 1972 it joined the new Faculty of Social Sciences which, while focusing on the Social Doctrine of the Church, has always paid great attention to all areas of social sciences: Sociology, Political Sciences, Economics, and Anthropology. It was only by chance that the Fund of the Social Sciences Seminary did not have the same fate as its counterparts: with its 8,000 works, it was in fact impossible to incorporate it into the section of the Book Tower Depository dedicated to Social Sciences, and was therefore located separately, first in an area adjacent to the historical reading room and then, in recent years, in the Traspontina Depository, where it has found a place next to the other special collections of the Library.

When the Second Vatican Council promulgated the Nostra aetate declaration, whose main theme was the relationship of the Catholic Church with non-Christian religions, with particular reference to the recognition of the religious sense in the life of each man and to the bond that links Christianity to Judaism, a group of bishops and experts met to discuss its application: it’s the birth of the SIDIC (Service International de Documentation Judéo-Chrétienne, Jewish-Christian International Documentation Service) and its specialized library. In 2002 SIDIC moved its headquarters to the Pontifical Gregorian University, where the Cardinal Bea Centre for Jewish Studies has been carrying out a consolidated and recognized scientific and research activity in the field of Jewish Studies since 1979. With the closure of the Documentation Service, effective from July 15^th, 2009, the religious Congregation of Our Lady of Sion, which has always been the custodian of SIDIC, donated the collected documentary patrimony to the Pontifical Gregorian University, expressing the desire that this legacy should be maintained in its unity and made available to the public. On September 8^th, 2009, the Rector formalized the acceptance to welcome and integrate the documentary patrimony of SIDIC in the Gregorian Library; more than 6,000 documents are therefore transferred and in the following months they are gradually integrated into the catalogue. Today the SIDIC Fund, the only current one among Library’s special funds, is kept in the Traspontina Depository and has reached the consistency of about 8,000 volumes; it represents one of the most important libraries on the subject of Jewish-Christian relations, contributing significantly to the research in the field of Jewish Studies.

The Fund originates from the private library of Giuseppe Vedovato, a scholar of international politics and historian of legal institutions, who was Deputy from 1953 to 1972 and Senator of the Republic from 1972 to 1976 and had many years of experience at the Council of Europe, of which he was Honorary President; in short, he was a man who has played a leading role in Italian and European culture for over half a century. Generous benefactor of the Pontifical Gregorian University, in 2001 he donated to the Library his private collection of about 4,600 volumes and the complete collection of the Rivista di studi politici internazionali, a journal founded in Florence in 1934 of which he was director from 1947 to 2005. The trait that best distinguishes this Fund is its international openness and the precise design it reveals in its structuring: to contribute to a better knowledge of European and world ideals and realities in the subject fields of Law, Constitution, Diplomacy, History, Political and Social Sciences, and Economics, without any preclusion towards different cultural orientations. The Vedovato Fund is kept in the Traspontina Depository together with the other Library’s special funds, enriching with its focus the main Collection in the Humanities and Social Sciences fields. Thinking about this insertion, in the presentation of the printed catalogue of the Fund published in 2005 Vedovato recalls a suggestive vision of a library taken by Robert Musil: «Having entered that colossal profusion of books, it seemed to me that I had entered the interior of a brain; all around nothing but shelves with their cells of books; books upon books; there really was a smell of cerebral phosphorus, and I don't think I'm deluding myself if I say that I had the impression of having arrived at something». And it is precisely by using this powerful image that he wishes the present and future users of the Fund to investigate and use it with the certainty of “having arrived at something”.

In the two-year period as honorary President of the Council of Europe in 1987-1988, Giuseppe Vedovato gathered in Strasbourg an important book collection whose thematic centre is the Europe of the twentieth century. This collection documents the key events of twentieth-century history and their influence on contemporary society; ample space is given to historical-political reflection and to Europeanism, as well as to scientific and publicity material on the theme of the "greater Europe", a construction based on common Christian roots and the ideals that refer to Christian spirituality. The fund, resulting from two private collections purchased by Vedovato, was constantly enriched over the years and immediately became an important documentation and research centre. Having founded the Permanent Seminar on Ethics of International Relations in May 2003 at the Faculty of Social Sciences, in 2007 Vedovato donated the entire documentary collection kept at the Palace of Europe in Strasbourg to the Library of the Pontifical Gregorian University, thus recognizing its vocation to universality and its fidelity to the intention of Ignatius of Loyola, who conceived it as “Universitas Omnium Nationum”. The collection that reached Rome from Strasbourg almost doubled compared to the original nucleus; in 2008 the cataloguing started and continued for five years until the complete integration of the works in the documentary patrimony of the Library. In March 2012, a few weeks after Vedovato's death, a thematic Bulletin was printed to honour his memory on the occasion of his 100th birthday. The BEV Fund (Biblioteca Europea Vedovato, European Vedovato Library), whose consistency is around 18,000 volumes, has now found a place in the Traspontina Depository alongside the Vedovato Fund and the other Library’s special collections; its presence in Rome, where numerous international institutions and organizations are based and deal with the themes covered by this collection, represents an important opportunity for study and research, thus remaining faithful to the cultural project of its founder.

The Fagiolo dell'Arco Fund, donated to the Gregorian Library in 2006 by Maria Beatrice Mirri, has enriched the Library's documentary patrimony on Fine Arts, a subject field with an ancient tradition in academic studies. This sector is quite relevant within the Library collection and that’s why the "baroque library" by Maurizio Fagiolo dell’Arco was donated. The Fund fully reflects the cultural and artistic interests of its creator, a distinguished art historian, collector, and bibliophile: the collected works clearly trace the paths of his professional history and indicate the cultural contents of his activity, both in the context of art studies and collecting. The thematic fulcrum of the Fund is the Baroque, retraced through the numerous catalogues of the artists who were its protagonists and investigated in all its aspects, some of which, such as the "baroque party" and the "ephemeral apparatuses" that characterize it, unpublished and brought to the fore thanks to the studies of the same Fagiolo dell'Arco. Although the works tell of the extraordinary artistic season of Baroque both in its Italian and European evolution, there is a clear desire to pay above all homage to its Roman declination, considered one of the most shining manifestations of this style. The same coordinates are attributable to the writings on the Society of Jesus and on the fundamental contribution that Jesuits gave in defining the artistic style of the seventeenth century. Rome in particular, the privileged stage of the "baroque party", is also the background to the numerous volumes that illustrate the magnificence of churches, villas, palaces, monuments, squares, and fountains. There are also many works that trace the history of collecting starting from the sixteenth and seventeenth century, a theme very dear to Maurizio Fagiolo dell'Arco, who has always cultivated his collecting vocation not so much for his own pleasure, but to contribute to the dissemination of culture and artistic sensitivity. The collection, of which the catalogue was published in 2010, consists of approximately 3,000 volumes and is kept with the other special collections of the Library in the Traspontina Depository.

The Ancient and Rare Fund, legacy of the Bibliotheca Maior of the Roman College, consists of about 35,000 volumes including ancient printed editions, rare and valuable modern editions, and Ancien Régime periodicals. The first book nucleus of what will become the Bibliotheca Maior of the Roman College dates back to the second half of the sixteenth century. The collection grow over the centuries in line with the prestige of the College and formed the basis of the new Jesuit Library installed in the headquarters in Piazza della Pilotta in the early 1930s. The annexation of Rome to the new-born Italian State in 1870 and the confiscation law of the ecclesiastical axis brought part of the Bibliotheca Maior into the Biblioteca Nazionale Centrale (National Central Library) of Rome. What was saved from the requisition was stationed for a few decades in Palazzo Borromeo, increased in an outburst of revenge on the dispersive act, and finally moved to the new university building in 1930; according to the sources of the time, at the inaugural act the new Library consisted of 150,000 volumes and was made up in part of what was once called "Reserve", today known as the "Ancient and Rare Fund". As for the contents, in its perfectly balanced and transversal subjects covered the collection testifies to the broad interests and intellectual curiosity that have always characterized the studies and research of the Jesuits. Its oldest core is made up of 50 precious incunabula, the catalogue of which was published in 2008. The Ancient and Rare Fund, the noblest of the Library’s special collections, has recently been recovered and is kept in a controlled environment in the Traspontina Depository.