The chapter examines the way in which religious institutions in Czechoslovakia and then the Czech Republic have dealt with the legacy of the autocratic rule imposed by the Czechoslovak Communist Party and its repressive state institutions. It focuses on the brief post-Velvet Revolution Czechoslovak state of 1989–1992, when the policy was largely common for the Czech and Slovak parts of the federation, and then on the Czech Republic. The primary subject of this investigation is the impact of transitional justice on the country’s Roman Catholic Church which, despite the persistent erosion of its status in the society, has remained by far the most important religious institution in the Czech Republic. Key themes examined are the Communist repression, clerical resistance to and collaboration with the Communist regime, lack of religious lustrations, church rehabilitations, and memorialization, as well as the issue of restitution of church property.