St. Vitus Cathedral has two organ casings. The upper facade belonged to a baroque organ, which was built in 1765 by Anton Gartner. It had 40 stops on 3 manuals and pedals. This case is purely decorative. The associated work was transported around 1909 and was lost.

The lower neoclassical casing contains today's main organ. It was built by Josef Melzel in the years 1929–31. A general overhaul was carried out by the organ builder Brachtl a Kánský (1999–2001).[4] The rather modest instrument in relation to the large church space has 58 stops on 3 manuals and pedals, 4,475 pipes in total. The action is purely pneumatic. With a large number of basic pipes (flutes and principals) and little reeds (trumpets), the instrument has a rather gentle tone – a typical feature of post-Romantic organs.