The study of music of the later period (c.1600-1950) is one of the foundations of European musicology, including Czech musicology. The object of interest is not only music itself, but also its theoretical reflection, its historical, cultural and social contexts. The basic approaches consist of traditional and new historiographical and music-analytical approaches, enriched by the perspectives of philosophy, aesthetics, and musical practice. The actual scholarly work of the students of the Institute of Music takes place mainly within the historically oriented seminars, which, despite the considerable breadth of chosen topics and approaches, are characterized by an emphasis on original source research and bohemian contexts.

The Seminar on 17th and 18th Century Music, led by Marc Niubo, focuses on two main areas, namely sacred music of the High Baroque period and Italian opera in Prague in the 18th century, while other related topics, including instrumental music, are also treated to a lesser extent. The musical culture of the 19th century is explored and the history of music criticism and aesthetics is dealt with by Markéta Štědronská.