The Croci dipinte (painted crosses) cycle represents 12th and 13th century painting, all deriving from the oldest town churches, with works by Berlinghiero Berlinghieri, Giunta Pisano and the Master of San Martino.

The 14th and 15th century painting section features works by Francesco di Traino, Lippo Menni, Buonamico Buffalmacco, Spinello Aretino, Taddeo di Bartolo and other great painters of the age. Further 15th century works are represented by Masaccio, Gentile da Fabriano, Beato Angelico, Benozzo Gozzoli and Domenico Ghirlandaio, glazed earthenware by the Della Robbia school of art and the renowned bust-relic of San Lussorio, by Donatello.

The  polyptych by Simone Martini, from the Church of Santa Caterina d’Alessandria, the Natività by Tino di Camaino and the Madonna del Latte by brothers Andrea and Nino Pisano are considered masterpieces of 12th-15th century Pisan sculpture.

The museum also displays important low relief wooden sculptures. The 13th and14th century pieces feature works by the Sienese Francesco di Valdambrino.

The illuminated manuscripts section contains pieces from the 12th and 14th century, including the illustrated bible, Bibbia di Calci, dating back to 1168.

There is also a noteworthy collection of medieval Pisan and Islamic ceramic basins that were once used to decorate the external walls of the Pisan churches and are evidence of the trade industry between the Maritime Republic and the North African countries.