The over 300 of paintings collected by Gian Giacomo Poldi Pezzoli still are the core of the museum's collections. From its very origins, the painting collection was not intended as an encyclopaedic assortment; rather, it was created as a precious anthology of works, mainly from the Renaissance, aimed to illustrate the history of figurative arts in Northern Italy as well as in some parts of Central Italy. In the collection there are important works by the Lombard followers of Leonardo (Luini, Boltraffio, Solario). And masterpieces by Pollaiolo, Piero della Francesca, Botticelli, Mantegna and Bellini. Equallly significant are the 18th century works by Guardi, Canaletto and Tiepolo. Finally, some19th century paintings and portraits are directly linked to Gian Giacomo Poldi Pezzoli, his family and the circle of artists, antiquarians and connoisseurs (Giuseppe Molteni, Giuseppe Bertini, Giovanni Morelli) he met.

The on-line catalogue of paintings has been realized within 2005 and 2008 thanks to the contribution of Ministero per i Beni e le Attività Culturali – Direzione generale per i Beni Librari e gli Istituti Centrali.