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Whichever stage of Muhlhausen's cultural and urban history you can see, St. Mary - main church of the upper town and the second largest hall church in Thuringia after the Erfurt Cathedral - played an essential role. Here, the imperial legal decisions were announced in the Middle Ages, here was the preferred burial place of the most respected personalities of the city, here the radical reformer Thomas Muntzer preached, here Princely Day was held, here the council election cantata of the young Johann Sebastian Bach sounded for the first time. Since then, the building, secularized in 1975, has served as a museum and muess memorial. A separate exhibition area is dedicated to the life and work of the preacher Thomas Muntzer, who spread his ideas here.

St. Mary's Church was originally built in 1460-1470 and enlarged in 1841-1845. In the church, there is an altarpiece from 1845 by Friedrich Ludwig von Maydell. The organ was built by Willhelm Müllverstedt in 1833. The church bell was cast in 1868 in Bochum, Germany. According to legend, a young girl named Mary was walled up in the church.

First mentioned in a document in 1232, the construction of today's St. Mary's Church began around 1290 and was completed in the mid-15th century. St. Mary's is a major work of the North German brick Gothic style.

St. Mary's Church is a stone church built at the end of the 15th century. The barrel-vaulted church hall has a rare painted floor. The church has not held regular services since 1913, but it is used as a "road church" in Finland during the summer and baptism and consecration services are held there occasionally. The Sastamala Gregoriana is an annual musical event held in the church.

St. Mary's Church, built in the 13th century, is considered a late Gothic masterpiece in Central Europe. Built on the model of the Marienkirche in Lübeck, it was from 1549 to 1647 (the date on which its gothic spire fell), supposedly the highest structure in the world. Very little of the original rich interior remains, the iconoclastic period of the Reformation and a great city fire in 1647 destroyed almost all inventory.

St. Mary's Church was built around 1600 after the demolition of St. Jørgen's Church. The tower, however, is a later addition completed in 1883. The church's furniture is marked by the taste of Duke John the Younger (1564 - 1622) for the Renaissance style.

St. Mary's Church is a Lutheran church that was built in 1842. The church burned down during the Second World War in 1941. After the war, it was rebuilt to become a gymnasium of the Estonian Agricultural Academy. In 2009, the building was returned to the congregation of St. Mary of Tartu, who started to restore the church to its old exterior but with a new interior.

The Basilica of the Visitation of the Virgin Mary, or simply the Church of St. Mary, was first built in 1409 under Vytautas the Great. The original Gothic style of the church derives from this first construction. The visible Baroque features came with later reconstructions in the 18th century, initiated after the church was damaged by the Great Northern War.

St. Mary's Church is a medieval stone church that would date back to the mid 15th century, probably to the 1440s. However, there have been several wooden churches in the parish, the oldest of which were built as early as the beginning of the 13th century. The walls and vaults of the church bear medieval paintings which, according to the historian Markus Hiekkanen, were painted by the church builders themselves.

St. Matthew Church is a Gothic brick church dating from the 13th century. First a Knights of the Cross monastery with a red star, it became an auxiliary parish church in the 19th century. Restored in the years 1895-1896, damaged during the battles of 1945, the church was neglected for a long time. It was finally rebuilt in the years 1961-1966.