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Thomas, James, son of Zebedee and Philip are the next group of three. Thomas is clearly upset; James the Greater looks stunned, with his arms in the air. Meanwhile, Philip appears to be requesting some explanation.

Matthew, Jude Thaddeus and Simon the Zealot are the final group of three. Both Jude Thaddeus and Matthew are turned toward Simon, perhaps to find out if he has any answer to their initial questions.

In the 19th century, a manuscript (The Notebooks Leonardo Da Vinci pg. 232) was found with their names; before this only Judas, Peter, John and Jesus were positively identified.

In common with other depictions of The Last Supper from this period, Leonardo adopts the convention of seating the diners on one side of the table, so that none of them have their backs to us. However, most previous depictions had typically excluded Judas by placing him alone on the opposite side of the table from the other eleven disciples and Jesus. Another technique commonly used was placing halos around all the disciples except Judas. Leonardo creates a more dramatic and realistic effect by having Judas lean back into shadow. He also creates a realistic and psychologically engaging means to explain why Judas takes the bread at the same time as Jesus, just after Jesus has predicted that this is what his betrayer will do. Jesus is shown saying this to Saints Thomas and James to his left, who react in horror as Jesus points with his left hand to a piece of bread before them. Distracted by the conversation between John and Peter, Judas reaches for a different piece of bread, as, unseen by him, Jesus too stretches out with his right hand towards it. All of the angles and lighting draw attention to Christ.

The painting contains several references to the number 3, which may be an allusion to the Holy Trinity. The Apostles are seated in groupings of three; there are three windows behind Jesus; and the shape of Jesus' figure resembles a triangle. There may have been many other references that have since been lost to the painting's deterioration.