Research is conducted at the Jagiellonian Library in the fields of source studies, book history, and the history of Polish culture from the 15th century to the 20th century.

Creating Catalogues. On the basis of special collections, specialised catalogues are designed. The most significant ones include: Katalog łacińskich rękopisów średniowiecznych Biblioteki Jagiellońskiej (Catalogue of Latin Medieval Scripts in the Jagiellonian Library), Inwentarz rękopisów Biblioteki Jagiellońskiej (Inventory of Manuscripts in the Jagiellonian Library), Katalog zbioru dyplomów pergaminowych BJ (Catalogue of the Parchment Diplomas Collection in the Jagiellonian Library), Katalog druków XVI w. (Catalogue of 16th-century Prints), Katalog starych druków XVII w. (Catalogue of 17th-century Prints), Katalog proweniencji i opraw druków XVII-wiecznych (Catalogue of Provenances and 17th-century Print Covers), Katalog najcenniejszych rysunków polskich XVII–XX w. (Catalogue of the Most Valued 17th-to-20th-century Drawings) and Katalog polskich druków muzycznych wydanych w latach 1800–1949 (Catalogue of Polish Musical Prints Issued Published from 1800 to 1949).

Studies on Hebrew Manucripts. A research project was conducted in order to create a database of Hebrew manuscripts. It was a part of the major project entitled Les livres dans les livres: les fragments hébreux dans les bibliothéques européennes – Books within books: Hebrew Fragments in European Libraries – in collaboration with L'École pratique des hautes études in Paris.

Texts on Medieval University of Kraków. Research that aims to develop a catalogue of medieval Latin manuscripts, as well as research in medieval education and teaching.

Manuscript Heritage after Michał Pawlikowski (1887–1970). An inventory of the manuscript collection from Michał Pawlikowski's home archives containing valuable materials on the history of Polish literature and culture. Two volumes of the inventory have already been published; additional volumes are in development.

Orientalia Polonica Series. A project devoted to documenting Polish research traditions on the Orient is being carried out in collaboration with the Faculty of Philology and the Faculty of International and Political Studies. One of the project's objectives is to digitalise the source material and make it available on the Jagiellonian Digital Library platform, as well as to examine selected works and prepare them for publication.

The staff of the Manuscript Section of the Department of Special Collections participates in studies that are conducted at the Faculty of Philology of the Jagiellonian University in the area of Romance-language manuscripts collection from the "Berlinka" collection of the Jagiellonian Library.

Prof. Zdzisław Pietrzyk – studies the history of culture, the Church and Reformation in the 16th and the 17th centuries, the research journeys Polish students took abroad in the 16th and 17th centuries, and the history of the Jagiellonian University. Prof. Pietrzyk's field of research covers cataloguing and editing historical sources, including the modern manuscripts in the Jagiellonian Library.

Dr Marian Malicki – his domain includes studies in print culture (and typography) and book history in the 16th and the 17th centuries, "Polonica" in foreign libraries, the provenance of the 16th-century prints in the Jagiellonian Library, as well as editing and cataloguing prints from Jan Brożek's collection.

Dr Monika Jaglarz – her interests include compiling manuscripts and editing modern sources, such as documents which concern the historical demography of Poland, as well as the history of books and bookselling in Poland, particularly in Kraków, in the 16th and the 17th centuries.

Dr Wojciech Świeboda – explores medieval Latin manuscripts, conducts research in medieval diplomacy and the history of religious dissidents. He is the co-author of the catalogue of the parchment diplomas in the Jagiellonian Library.