Originally, there stood three organs in St. Nicholas's Church and their maker was a lay member of the Jesuit Order called Friar-organifex Tomáš Schwarz. His organs also decorated the interiors of many other non-Prague Jesuit churches. Proof of Schwarz's exceptional skills and his largest instrument is the large organ with 3 fingerboards and 44 registers placed in the west organ loft of the Church of St Nicholas, Lesser Town, Prague. It first sounded on October 10, 1746.
It is interesting to know that this organ was put into service at a time when the Church bldg had not as yet been quite complete and the nave was closed by a temporary wall on which an illusive altar was painted. Consequent building activities in the Church interior did not quite agree with the organ, for example, the temporary wall was pulled down after the nave and dome diagonal crossing was completed and the jack arch was chiselled away to make room for an extensive fresco by Lukáš Kracker above the nave (1760).
In terms of sound the organ was a representative of the then-considered usual type of the so-called South-German organ. What was unusual was the freestanding musical table, which had just begun to be constructed instead of the musical tables that had been built directly into the organ case.
The year 1802 was fateful for Schwarz's organ because it was in this year that a German musical theoretician Father Jan Vogler came to Prague to present his facilitation system. This system simplified the playing of the organ. Unfortunately, it also simplified its sound. The purpose was for the organ to substitute the sound of an orchestra. Even though Father Vogler gained great respect from music experts, it was not long before people realised that the organ had lost a lot of its original sound and that the experiment did not benefit the organ. People wanted the organ to be repaired.
It was only in 1835 that an organ builder Josef Gartner tried to return to the organ its original sound. The pipes removed by Vogler had got lost and it was necessary to make a whole lot of new pipes. Nevertheless, the beginning of Romanticism changed the sound of the organ to meet the spirit of the so-called Cecilian Reformation.
In 1904 an organ builder Josef Hubička replaced a number of higher trace-length registers with stylistically inappropriate equal voices. The organ remained in this state until another questionable reconstruction completed in 1959 under the leadership of Prof. J. B. Krajs. The aim of this reconstruction was to give the organ its original sound variation and at the same time to extend it to make it a gigantic organ with four fingerboards, similar to the organ in St. Jacob's Church in Prague in 1702. Due to insufficient financial means a new musical table was acquired, sections of the original mechanical tracture were removed, electric magnets controlled tone valves, new air locks were added to extend tone ranges, and lower octaves were hard-plated.
Nonetheless, it may still be said that even after the above-mentioned interventions, the entire instrument was professionally renovated in a style that is usual in the present world of instruments of a similar type. Only a few three-fingerboard Baroque organs have been preserved in the Czech Republic and that is why the St. Nicholas organ deserves the peculiar care.
While we can admire Tomáš Schwarz's large organ with its beautiful organ case decorated by an angel choir and a preserved musical table, his smaller two-fingerboard organ with 18 registers stands in the left gallery above the dome in St. Michael's Church in an undamaged state of sound. This organ was originally placed in the west gallery, next to the Virgin Mary of Foyen altar and was used for parish and school masses. It was renovated a few years ago and today serves primarily concert purposes.
Tomáš Schwarz's third organ was most probably placed into the right gallery of the Church and had one fingerboard and 13 registers. It was transferred to the Church of Marie Snežná in 1832 and then disappeared.

Jesuit halls of residence and lectures always played a significant role in the musical life of cities and that is why even in the Church of St. Nicholas care was taken to ensure the ultimate quality of musical productions during Mass. Church music was always conducted by praefecti musicae from the Jesuit Priest Order until the Order was terminated by Joseph II. Then the Choir and the Orchestra of St. Nicholas's Church were conducted by temporary prominent composers, such as Vincenc Mašek (1795-1831) and the organ was played by František Xaver Brixi before 1759, Karel Pitsch (1832-1858) and Josef Foerster (1858 -1861), to name at least some.
Shortly after W. A. Mozart's death, Prague paid tribute to his memory through performance of his famous Requiem in the Church of St. Nicholas by members of the Prague Theatre Orchestra.