It was the second site after Italian rock engravings in Valcamonica to be classified as a World Heritage Site by UNESCO, along with the fresco of the Last Supper by Leonardo da Vinci, which is in the refectory of the convent.
The aisles, immersed in the twilight, were lighted by Bramante with a monumental tribune , covered by a hemispherical dome. He also added two large lateral apses and a third, over the choir, in line with the aisles. The ordinate scanning space is also reflected on the outside, in an interlocking volumes that culminates in the lantern that masks the dome, with a loggia that is linked to the grounds of early Christian architecture and the Lombard Romanesque.

The refectory of the Convent of Santa Maria delle Grazie forms an integral part of this architectural complex. On the north wall is The Last Supper, the unrivalled masterpiece painted between 1495 and 1497 by Leonardo da Vinci, whose work was to herald a new era in the history of art. The fresco was commissioned in 1495 and completed in 1487. The representation by Leonardo da Vinci depicted the moment immediately after Christ said, 'One of you will betray me'. The 12 Apostles reacted in differing ways; their movements and expressions are magnificently captured in Leonardo's work. He focused on the impact of Christ's words on the Apostles and on their reactions. This broke with the traditional representation of the past, upsetting some ideas. The genius of the artist is seen especially in the use of light and strong perspective. The three windows behind the table companions and the landscape beyond create a luminosity that set against the backlight illuminates the characters from the side as well. The result is a combination of a particular classically Florentine and chiaroscuro perspectives.

The Last Supper by Leonardo da Vinci embodies in its harmonic prime the knowledge of an era through a esoteric symbolism: the knowledge of the universe, alchemy, science, the man and God.
The Apostles are grouped to represent the seasons and each refers to a specific zodiac sign and a specific constellation, while the posture of each reveals the antinomy between opposite signs; groupings also allow to identify the ternary and quaternary; Christ is at the center of the perspective to represent the Sun, origin and harmony in the world, as well as a symbol of the Great Work; the location and movement of each Apostle corresponds to a certain color and certain musical notes; the positions of the hands is similar to a musical score in the key of C; the architectural environment in the fresco painting responds to precise geometric and mathematical rules.