The first Tomb of Pope John Paul II, who's funeral was held on April 8, 2005, was on the north side of the Grottoes, less than 100 ft from the Tomb of St. Peter.  John Paul II was interred in an area that had held the sarcophagus of Pope John XXIII. After being declared Blessed in 2000, John XXIII's body was transferred up to the St. Jerome Altar in the basilica on June 3, 2001.

On May 1, 2011 John Paul II was moved under the Altar of St Sebastian after being declared blessed.

John Paul II was laid to rest in a cypress coffin, which served as the innermost of the three traditional coffins. This was placed into a larger solid zinc casket, which was soldered shut. This coffin was adorned with three bronze plaques: a simple cross at the head of the coffin, a middle plaque with the Pope's name and the length of his life and pontificate, and a third with Pope John Paul II's personal coat of arms at the foot. The zinc casket was finally lowered into a larger walnut (traditionally elm) casket, bearing three identical plaques, which was shut with nails of pure gold.