The subject of the article focuses on broader problem of the ‘confessionalization’ of Early Modern architecture or the specifics of sacred architecture in post-Reformation Europe. The study is based on the Czech environment in the 16th and the beginning of the 17th century. Several sacred buildings, both non-Catholic and Catholic, were founded with special relation to the environment of Rome. The remarkable environment of Rome, which in the sixteenth century again became a central and reference location for artistic and religious work in Early Modern Europe, could for various reasons inspire both main religious groups. In addition to Catholic churches, the study also looks at the churches of the Unity of Brethren as a unique denomination in the Czech lands. As the most remarkable examples serves the Unity of Brethren church in Mlada Boleslav, seat of one of the bishoprics (later called as “Rome of the Unity of Brethren”). On the other hand the ties to Roman prototypes are observed among Catholics in the case of Olomouc, the seat of bishops of Moravia where the confessional architecture became a special tool of Counter-Reformation gesture.