Jogaila began to build Sts. Johns' Church as the first centre of the Catholicism immediately after Lithuania's conversion to Christianity (1387 - 1426 m.). At first, it was in the gothic style, elements of which style are still evident in its inner space. In 1571, the church was taken over by the Jesuits and it has been a part of the University complex since that time. It was one of the most beautiful churches in Lithuania. This church is one of the witnesses of Lithuania's famous past: the Grand Dukes of Lithuania Steponas Batoras, Zigmantas III, Vladislovas IV, and Jonas Kazimieras as well as the Russian Tsar, Peter the Great, were received in state there.

The architecture of the building is extraordinarily impressive, i.e. the baroque style fasade, which forms a symmetrical composition, and the sharp wavy forms that are reminiscent of a huge organ. The tympanum of the church's late baroque style rear fasade is also composed of very plastic forms. The Sts. Johns' church is especially charming on a sunny day. Vilnius has no other building where the play of baroque shadows is so perfect.

A great presbyter altar, a unique composition of ten smaller altars and the only one in Lithuania and the Baltic States, occupies a special place in the church's interior. This is a masterly baroque 18th century work with the altars situated in an arc on different levels, on which the light falls through the rear windows of the presbytery. All the altars are abundantly adorned with paintings and sculptures.

The bell tower (68 m or 223 ft) of Sts. Johns' Church was built in 1571 and is even higher than the Cathedral's. It has both baroque and renaissance features. The cross on top of the bell tower was made by local smiths in the second half of the 17th century. At present besides services, the church hosts concerts and small-scale events and also houses a museum.