The funeral started off with an intimate ceremony, attended only by the top Vatican prelates in St. Peter’s basilica, who placed a pouch of silver and bronze medals and a scrolled account of his life in his coffin. Archbishop Stanislaw Dziwisz, John Paul's long-time private secretary, and Archbishop Piero Marini the master of the liturgical ceremonies, placed a white silk veil over the pope's face and sprinkled his corpse with Holy water. Psalm 41 (42): "As the deer longs for streams of water, so my soul longs for you, O God." was recited as the cypress coffin was being closed.

The funeral Mass started at 10:00am local time (8:00am GMT) on the steps and lasted for about two and a half hours. The coffin was placed before the altar and was closed.

The German Cardinal Joseph Ratzinger, deacon of the College of Cardinals, presides on the service. He was joined by 164 cardinals and patriarchs of the Eastern Rite Churches, all clothed in red vestments. These took place on his right in the 600-seat clergy section. About 1400 Italian and foreign dignitaries took their place on his left-hand side. In front of him were the former leaders of state and government, ministers and other important guests.

The Mass started with the introductory hymn, "Eternal Rest Grant Him, O Lord," followed by the singing of Psalm 64 "To You We Owe Our Hymn of Praise, O God of Zion."(sung in Latin)

After the hymn the reading of a prayer for the Pope took place.

The first reading of Scripture was Acts of the Apostles 10:34-43 (in Spanish), where Peter holds a speech about God’s equal treatments towards all people in front of Cornelius. Followed by Psalm 22, "The Lord is my Shepherd, I shall not want." (in Latin)

The second reading was Philippians 3:20-4:1, "But our citizenship is in heaven;"(in English) After this followed John 6:40, "For this is the will of my father that everyone who sees the son and believes in him may have eternal life;" and John, 21:15-19, which is a dialogue between Jesus and Peter, where Peter is being told to feed the Lord’s sheep.

The German Cardinal Joseph Ratzinger delivered the homily.

Then the Consecration followed, performed by Cardinal Joseph Ratzinger, where he prayed over the Consecrated Bread and the chalice of wine, which represent the Body and Blood of Jesus Christ.

The next thing is the Holy Communion song, Psalm 129, "Out of the depths I cry to you O Lord, Lord hear my voice."

When the Communion had finished, a rite of Final Commendation and Farewell was performed, during which cardinals approached the coffin and Cardinal Joseph Ratzinger led the prayer with the words: "Dear brothers and sisters let us entrust to the most gentle mercy of God, the soul of our Pope John Paul II. ... May the Blessed Virgin Mary ... intercede with God so that he might show the face of his blessed Son to our Pope, and console the church with the light of the resurrection."

A choir sang the Litany of the Saints after the prayer, a long list of saints asked to pray for the Pope’s soul (The names of saints declared as saints by John Paul II might be added to this list). Then Cardinal Camillo Ruini, a Roman Catholic priest of Rome, finished the litany with a short prayer.

The patriarchs, the archbishops and the metropolitans of the Eastern Rite churches approached the coffin after Cardinal Ruini had returned to his place and prayed for the soul of the deceased pope and blessed the pope with incense.

A moment of silent prayer followed. Then Cardinal Ratzinger sprayed holy water on the coffin and blessed it with incense. He ended the funeral Mass with a last prayer before everyone stood up and sang together, "May the angels accompany you into heaven, may the martyrs welcome you when you arrive, and lead you to Holy Jerusalem."

Then prelates left the altar in procession, accompanying the coffin down the steps of St. Peter to the Vatican grotto where the burial rites will follow. During this period, Psalm 113 A (114), "When Israel came out of Egypt", Psalm 117 (118), "Give thanks to the Lord, he is good" and Psalm 41 (42), "As the deer longs for streams of water, so my soul longs for you, O God." will be sung by the choir.

The coffin will be closed and sealed with both papal and Vatican seals. After that the coffin be placed in another coffin of zinc that is hermetically sealed. This zinc coffin will be placed in a third coffin of oak. This outside coffin bears the name of the pope, his cross and his papal coat of arms. Cardinal Eduardo Martinez Somalo will lead the prayer during this happening. The end is the singing of the hymn, "Salve Regina."