The Grand Courtyard is the pantheon of the University, whose gallery commemorates the University's founders, patrons and eminent men of service. The surviving frescoes ot the northern wing of the building display the VU coat of arms and portraits of the University's patrons, while the highlight of the structure is the magnificent early 14th century baroque portal of the parochial St. Johns Church. After the fire in the middle of 18th century, the church and belfry were reconstructed in late baroque style by the most eminent architect of the Grand Duchy of Lithuania, Jonas Kristupas Glaubicas.

The Astronomical Observatory Courtyard boasts a 18th-century observation building with signs of the zodiak on it. The former site of a chemist's shop now features a memorial plaque to Rector of Vilnius University, head of the Observatory, corresponding member of the Academy of Sciences of Paris and member of Royal Astronomical Society of London, Martynas Pocobutas. The courtyard has formed on the site of a former garden, with a surviving early 16th century Gothic house of Mikalojus Jasinskis next to it.

M.K.Sarbievijus Courtyard Educated at Vilnius University to become its proffesor, Motiejus Kazimieras Sarbievijus was an eminent early 17th century European poet. The courtyard, bounded on four sides by buildings reminiscent of different styles and epochs, houses the Littera bookshop in a vaulted room frescoed by the painter A.Kmieliauskas. Next to it is the University's Lithuanian philology centre, frescoed by the painter P.Repsys.