The cuspidate Madonna dell’Idea by Michelino da Besozzo, dating back to the second decade of the 15th century, is a work of great value. The majority of the paintings displayed in the museum go back to the Borromean period (15th-17th century).

The richness of this historical period is testified by the Miracle of the Parturient by Giovan Battista Crespi, known as Cerano, forming part of the cycle of the Miracles of San Carlo Borromeo. An oval with San Carlo in Glory is by the same author; the painting with a sorrowful San Carlo carrying the Holy Nail in procession is by Fede Galizia and two large paintings dedicated to San Giovanni Buono are by an anonymous Lombard master of the early 18th century. An early painting by Tintoretto depicting the Dispute of Jesus with the Doctors in the Temple comes from the collection of Cardinal Monti.

There are also some splendid monochromes by Cerano dedicated to the Creation of Eve and the heroines of the Old Testament: Esther and Ahasuerus, Judith and Holofernes, Solomon and the Queen of Sheba, Jael and Sisera, which were intended to be produced in marble for the overdoors of the Cathedral.