The Department of Musicology focuses its research activities on Bohemian aspects of the history and theory of music between the seventeenth and twentieth centuries. The members of the department develop their own topics formulated in accordance with the research priorities of the Institute, while the department is also starting work on a framework team task aimed at researching concert life in the Czech lands. Regular events include an international conference on eighteenth-century Italian opera (Český Krumlov) and a symposium on current issues in Mozart research (Prague) organised by Milada Jonášová. The department also runs the lecture series Dialogo della musica. A number of projects within the framework of the AV21 Strategy programme have addressed or are still addressing the issues of thematic catalogues and inventories (Václav Kapsa), the Prague Mozart villa Bertramka (Milada Jonášová), women in 19th century Czech musical culture, concepts of identity in Czech cultural life in times of crisis with a focus on (semi)private space (Anja Bunzel) and Czech operetta with its international contexts (David Vondráček).
Within the Artefactum publishing house, the department produces the critical series Academus Edition, and papers from conferences on Italian opera are published in the series L'opera italiana nei territori boemi durante il Settecento published by Academia. The Department of Musicology is the seat of the editorial office of the scholarly musicological journal Hudební věda (Roman Dykast, Markéta Janková).
The department is currently working on two projects of the GA ČR: The Development of Popular Music Research in the Czech Lands in the Context of Central European Culture and Politics since 1945 (with Palacký University in Olomouc, researcher Aleš Opekar, 2021–2024) and Semi-Private Musical Practices in Prague, Vienna and Berlin (1815–1850): Musical Repertoire within the Socio-Cultural Context of the Time (1815–1850) (researcher Anja Bunzel, 2022–2024).
The department provides facilities for researchers applying for the Josef Dobrovský Fellowship. The department's staff collaborates with a number of academic institutions, including universities, and participates in the work of grant committees and editorial boards of discipline-specific journals.