According to Leonardo's journals, the year 1490 marked the arrival of a new member to the artist's household: the ten-year-old boy Giacomo, known as "Salai." Salai was a beautiful boy from a peasant family. No one knows the precise nature of his relationship to Leonardo, though the master seemed quite indulgent toward him, showering him with gifts and never punishing him for his constant petty thievery. Salai lived with Leonardo for the rest of his life. However, they often quarreled, and for one reason or another, Salai seems to have received less at Leonardo's death than seems appropriate.

In 1493, a woman named "Caterina" came to live with Leonardo. Although historians remain unsure whether this woman was Caterina Leonardo's mother– she may have been a servant–but many scholars suspect she was indeed the artist's mother: some of the few vague personal notes in Leonardo's notebooks suggest that he had invited her, as opposed to hiring her. Also, the Caterina that came in 1493 died a few years later, and this would have made sense given his mother's age; moreover, in Leonardo's day mothers often came to live with their children after their husbands' deaths. However, Leonardo's accounts show that he spent curiously little on her funeral. He may have wanted to avoid a conspicuous funeral, not wanting to draw attention to his illegitimacy and dishonor his mother.

In 1495, Leonardo began work on a large wall painting for Sforza. Twice a week, Sforza ate dinner in the refectory of the convent of Santa Maria delle Grazie; he wanted a large portrayal of Jesus' Last Supper to hang on the wall facing the head table.

The Last Supper and the Mona Lisa are easily Leonardo's most famous paintings. Of the millions who have seen reproduction of the The Last Supper, few realize that it is not only a masterful painting, but also a cheap optical illusion! Painted on the wall of a refectory (or convent dining room), it was in fact intended to appear an extension of the room itself; the effect is achieved by the painting's perspective, which matches the lines of the room. Thus the table of Christ floated above the heads of the dining monks. The perspective serves other purposes as well: its lines focus on Christ's head, which is cleverly framed by an open window–a kind of circumstantial halo. The pious would say that Leonardo wanted to show that Jesus's natural grace provided him with this divine framing, that Leonardo eschewed painted gold discs because they were artificial. The German writer Goethe, however, suggests that Leonardo left out halos as a gesture toward secularizing the myth of Jesus. At any rate, Leonardo took special care to follow scriptural details; the seating arrangement reflects the Bible's description, though to achieve this Leonardo flew in the face of traditional quatrocento arrangements, which had Judas sitting on the opposite side of the table. Here he is the third man to Christ's right; he clutches a moneybag. Christ forms a regal triangle with his body, like the Virgins of Adoration of the Magi or Virgin of the Rocks; his disciples form rippling waves. He has just announced that one of them will betray him, but he has not yet indicated that it is Judas. Each disciple is eager to acquit himself or identify the future traitor. Grouped into threes, the disciples on the far right recoil in surprise, while the next group leans toward Christ with curiosity; each group has a slightly different reaction to the news. Generally, the hands of the disciples contradict the movement of their bodies, giving the whole composition a flowing circuit that always leads back to the center. As in the Adoration of the Magi, Leonardo shows his ability to animate a scene that had become clichéd through countless previous depictions.

Because his master, Verrocchio, had not been an expert in wall painting, Leonardo himself lacked significant knowledge of the correct technical process. He tried to invent his own paint mixtures, but he insisted on painting with oils, which do not suit wall painting. As a result, the painting began to deteriorate almost immediately.

While Leonardo was working on The Last Supper, the famous mathematician Fra Luca Pacioli came to stay in Milan. As an illegitimate child, Leonardo had been denied secondary education, and thus could not perform even simple algebra. However, he had always had an interest in numbers and math, and he eagerly learned from Pacioli; Pacioli for his part must have shared a mutual awe for his pupil: Leonardo was already the author of so many designs and discoveries. The two even collaborated on a book, De divina proportione, Leonardo supplying the illustrations. Also at this time, Leonardo decorated the La Sala delle Asse.

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