- Convent of Santa Maria delle Grazie. Where The Last Supper is located.
- Church of Santa Maria delle Grazie. Its dome was designed by Bramante.
- Church of San Francesco il Grande, place of The Virgin of the Rocks, also called "Maestà".
- Sforza Castle. Home and Headquarters of Ludovico il Moro family. Inside its walls is the Rochetta Palace, where Beatrice d'Este died.
- Concorezzo, little village north of Milan. It was the refuge for the last cathars in XV century. See map.
- Monastery of Santa Marta, home of Sister Veronica da Binasco, the prophetess.
- Piazza Mercanti, scene of one of the crimes in the book.
- Palazzo Vecchio, place of the first exhibition of La belle Ferronière by Leonardo da Vinci.
- Monastery of Santa Maria sopra Minerva, headquarters of the Dominican Order.
- Bethany headquarters (also called House of Truth), on the Aventino hill (this is a fictional place).
- Vatican. Inside, there are the Borgia chambers, described in chapter 34.
- The Academy of Marsilio Ficino was in a Medici Villa at Careggi, in the north of the city.
- Cathedral. Here is the astronomical calendar designed by Toscanelli, described in chapter 9.