Pope Anacletus (76-88), Peter's immediate successor, built a small chapel over the Apostle's tomb. It immediately became a place of worship and pilgrimage for the early Christians, later popes and those who came to Rome in spite of the risks of the ferocious persecutions, so that could pray at the tomb of the Prince of the Apostles. The persecutions came to an end under Constantine, the emperor who had a vision of the Cross as a sign of victory. Under his reign the church's spiritual leadership was officially recognized with the famous Edict of Milan in 313. It was Constantine who, in 324, built a lavish basilica over the entire cemetery and part of the circus. The main altar was to stand over Peter's simple tomb. Legend tells us that the emperor removed his rich robes and began digging the foundations with his own hands. He personally filled and carried away twelve baskets of earth: one for each apostle.

The circus had to be destroyed to build the church (much of the circus structures were made of wood) and many tombs had to be removed and reburied.  According to Roman law, only the the Emperor, the supreme authority , could give permission to tamper with grave sites.. Then, to position the main altar over St. Peter's tomb, half the hillside sloping down towards the circus had to be excavated. The cuts in the hill are still visible to this day on the northern side, outside the Basilica.

The old, five-aisled basilica was 118 meters long, 64 meters wide and had 88 columns, that is, 22 in each row. It was begun in 324; the main portion was finished in just five years, and was consecrated by Pope St. Sylvester (314-335). Over the following decades it was embellished with a portico, that soon became a preferred burial place for popes, kings and emperors who wanted their final resting places near that of St. Peter. During previous centuries many simple faithful had been buried there, giving further proof of the authenticity of the legend that this is, indeed, the site of St. Peter's tomb. Later, a bell-tower, with 12 windows on each of its six storeys was built, as was a double-portico that was used for papal blessings. The basilica had 120 altars, 27 of which were, in some way, dedicated to the Virgin Mary .Of the 700 oil lamps, 120 burned around St. Peter's tomb. The basilica was a focal point of spiritual life: Peter and other early Christians were martyred on the site, and Peter was buried there. Peter's successors chose the site as their seat, and it was there that relics from the Holy Land such as the relic of the Holy Cross, St. Veronica's veil and the lance that had pierced the side of Christ were kept. The interior of the basilica was resplendent with rare marble, mosaics of all colors, shining metals, draperies, tapestries and precious stones. The floor around the tomb of St. Peter was covered with gold and silver. These priceless treasures were stolen when the shrine was sacked by the Visigoths (410), the Vandals (455), the Saracens (846), the Normans (1084) and others who, attracted by their material value, totally ignored their spiritual significance. In fact, the countless pilgrims who travelled to Rome from allover the world were not interested in gold or silver, they only cared about "videre Petrum ", seeing the shrine, strengthening their faith and enriching their spirit. In order to help this constant flow of pilgrims, the Scholae Peregrinarum sprang up around the old basilica; providing hostels and hospices for pilgrims of all nations: Frisians, Franks, Czechs, Teutons, Flemish, Hungarians, llIyrians, Saxons, Lombards, Armenians, and Abyssians, they came from Corsica and from north of the Po River and every other part of the world. Rome was becoming the patria communis. The opportunity to live, eat and sleep so close to the tomb of St. Peter, gatekeeper of heaven, for even a short time was considered a step towards salvation. This international "facility" had to close down when work was begun on the new basilica. The only Scholae that remained within the Vatican walls are the Teutonic Church and the Church of St. Stephen of Abyssinia. However, the glorious basilica, where twenty-three emperors had been crowned, that had welcomed pilgrims from every part of the world, that had celebrated the first Holy Year (1300), described by Dante and immortalized by Giotto's paintings, that had confirmed and strengthened Christian faith, began to show the ravages of time after twelve centuries. In the XVI century, after several attempts at restorations, the Basilica with its enormous history and traditions, was at risk. Reluctantly, the decision was made to demolish it, but on the brighter side, another decision was made, to erect an even greater one, the basilica as it exists today, on the same site.

In 1506 Pope Julius II laid the first stone of the new basilica and started construction that was to last for one hundred and twenty years. The greatest artists of the era worked on it: Bramante (1444-1514), Raphael (1483-1520), Michelangelo (1475-1564), Fontana (1541-1607), Della Porta (1540-1602), Bernini (1598-1680), Maderno (1559-1629) and others. Faith and genius paid homage to Peter's tomb and the new basilica, with its enormous dome reaching skyward, continues its hymn of praise to the greatness of God and the honor of St. Peter.