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His first tomb in the old basilica was located at the northern wall of the shrine of the Holy Veil. It was a simple coffin with a convex lid. Later, the elaborate funerary monument of Nicholas V was located at its side. The inscription on the front was a eulogy of Marcellus II and an excuse for the modest burial he was given. On September 15, 1606, the tomb was opened and the pope's body was found intact. It was then taken to the grottoes and deposited in a sarcophagus that had recently been found during excavations for the new basilica.

On the front of this ancient sarcophagus is the figure of the Savior with the scroll of the new law, standing on a rock with four mystic rivers flowing from underneath. The 2 figures of young men on the sides may represent the Disciples. On the sides are 2 strigilled panels and on the corners two figures of men holding scrolls who may represent the Apostles Peter and Paul and are looking toward Christ.

Engraved on the lid is the coat-of-arms of the pope and a brief inscription from 1606, dictated by the pope's nephew, Cardinal Bellarmine.

Under the sarcophagus is a Renaissance marble base with a plate in the center and fruit festoons on the sides. Immured above the sarcophagus is a marble plaque with the coat-of-arms of the pope.

In his 1955 guidebook to the Grottoes, Iohn de Toth stated that the figures on the corners of the 4th century sarcophagus were the likeness of the christian couple whose bodies were previously placed there.