But how close to the archaeological truth is this persistent tradition that St Peter's in Rome stands over the grave of the first pope? In Matthew 16:18 Jesus says to the apostle Simon, son of Jonah, 'You are Peter (Aramaic kepha or Greek petros – 'rock') the rock upon which I will build by church (ekklesia)'. Did this literally happen when Constantine erected the Christian basilica over an ancient cemetery on Mons Vaticanus overlooking the Tiber?

A remarkable archaeological detective story begins in the year the Second World War erupted, when work got underway to lower the floor of the crypt beneath St Peter's known as the Sacred Grottoes. In 1939 Pope Pius XI died and preparations were made to inter him in the crypt beside Pius X. The Vatican authorities decided to take this opportunity to convert the subterranean parts of St Peter's into a 'lower church' – a task which required the lowering of the floor to create sufficient height. As they dug downwards, the workmen first came upon the floor of Constantine's basilica – just 20 centimetres below the pavement of the crypt. Beneath that they broke into a street of ancient Roman tombs from the 2nd century AD, sloping eastwards down Vatican Hill. To the west the street, running directly under the nave of the basilica, headed in the direction of the current high altar. The whole city of the dead had been packed full of earth to form a gigantic horizontal platform upon which Constantine's basilica had been constructed. This was an enormous and costly feat of engineering which suggested to the Vatican archaeologists, appointed to investigate the find, that tremendous effort had been invested in building the basilica precisely at this spot. The four-man excavation team all belonged to the Papal Institute for Christian Archaeology and worked under the personal supervision of the Administrator of St Peter's Basilica, Monsignor Ludwig Kaas.

As Kaas and his colleagues worked their way westwards up the street of tombs, they began to find familiar early Christian motifs painted on the walls. Epigraphist Professor Margherita Guarducci was brought in and soon discovered a Latin graffito, painted on the wall of one mausoleum, which read: 'Peter, pray Christ Jesus for the holy Christian men buried near your body.' The inscription was dated to around AD 300.

Further on the excavators discovered an open court measuring 7 metres by 4 metres, bounded on its west (long) side by a thick red-plastered wall. Set into the face of the wall was an aedicula – an altar-like structure supported by thin columns. According to the surrounding archaeological evidence, this dated to around 160 AD – just a century after Peter's death. The team became very excited when they realised that the aedicula stood immediately below the high altar of St Peter's. The early Christian writer, Gaius (c. AD 200), had referred to the 'Tropaion of Peter' located on Vatican Hill. Latin scholars understood this to mean some sort of funerary monument standing over Peter's grave.

Kaas and his colleagues carefully proceeded to investigate the area beneath the red wall behind the aedicula. There they discovered an open space formed by an arch in the foundations of the wall. The brown earth of the tiny chamber's floor was sifted to reveal hundreds of coins from all ages and countries. These had been dropped down a narrow vertical shaft, the iron-grilled opening of which is to be found in the Niche of the Pallia where a new archbishop's pallium (garment) is left overnight before his induction. The Niche itself is located in the Confessio (a sunken area in front of the high altar) which lies on top of the courtyard of the aedicula. During the Middle Ages and earlier, the 5-metre shaft, just 13 by 20 cms, became a place of pilgrimage where the devout could 'make contact' with St Peter's mortal remains. Within the chamber at the bottom of the shaft the archaeologists also found human bones. At first they were convinced that they had found the remains of St Peter but, sadly, a later anthropological examination determined that there were in fact three skeletons – those of two young males and a much older female. None could have belonged to Peter who died at a mature age. The disappointment in the failure to find St Peter's bones reached all the way up to Pius XII who had been keeping a close eye on the secret search for the founder of his line … but then a remarkable thing happened.

The Vatican excavators had previously come across a 47 cm-thick buttress wall to the right of the aedicula, erected in the third century to support the red wall which had been showing signs of movement. The north plastered face of this buttress was covered in Latin names of early Christians who had presumably come to visit the original shrine to St Peter. A further investigation revealed that the wall contained a hidden repository, lined in marble. Unfortunately, the archaeologists found the hiding place empty – again no bones of St Peter. It was only in 1952 that the persistent delving of Margherita Guarducci uncovered an astonishing story which has to go down as one of the greatest archaeological blunders of all time.

A few months after the death of Ludwig Kaas a workman named Giovanni Segoni revealed to Guarducci that he and Kaas had returned to the shrine one evening in 1942, after the excavating team had gone home. Together they had opened the repository, exposed that day but, as yet, unexamined. Inside were several human bones. Kaas instructed Segoni to remove the contents and place them in a wooden box which was then hidden away in a storeroom. Of course, when the rest of the archaeologists came to investigate the repository, they found it empty. No-one was aware of what had transpired the previous night. To this day it is a complete mystery as to why the Vatican Monsignor, assigned the task of supervising the whole excavations by the pope himself, indulged in this clandestine operation. Kaas took his secret with him to the grave but, fortunately, Segoni was still there to take Guarducci to the storeroom in which the box lay forgotten and ignored. The bones were subsequently analysed and proved to be those of an elderly man of stocky build. A close examination showed they had once been buried in the soil beneath the aedicula and red wall. Red staining and fine threads of gold revealed that the relics had been wrapped in a fine woolen cloth, dyed in the emperor's purple and embroidered in gold. Whoever had been reburied in this secret repository must have been regarded with great esteem. Confirmation of the identity soon followed as, once again, fate played its part.

Back in 1950 archaeologist Antonio Ferrua had decided to re-examine the interior of the repository and, to his amazement, found that the previously empty container now held a new surprise. The fact is that the marble casing of the repository only covered the base and sides of the niche in the buttress wall. The upper part had been left open to the exposed bricks of the buttress and, at the short west end, the plaster of the red wall. A piece of that red plaster had been dislodged sometime since 1942, falling into the repository. Ferrua was immediately able to read letters scratched onto the surface of the plaster – letters which had been scribbled onto the inside west wall of the repository at the moment the bones had been sealed in their hiding place so many centuries ago. The Greek inscription read PETR[....] ENI. Two years later epigraphist Guarducci, having discovered that the repository had indeed held the bones of an old man, now realised the importance of this tiny plaster fragment. She translated the Greek graffito as 'Peter is within' or 'Peter is here'.

When was the shrine of St Peter founded? The 6th-century 'Book of the Pontiffs', Liber Pontificalis, claims that Pope Anacletus 'built and set in order a memorial shrine to the Blessed Peter, where the Bishops might be buried'. The problem is that Anacletus lived at the end of the 1st century AD – unfortunately too early for the erection of the 2nd century aedicula or Tropaion which is the visible monument for Peter's grave. However, there is another pope with a similar name – Anacetus – whose pontificate was around AD 155-65. It could well be that the writer of the Liber Pontificalis made a simple error and that the foundation of the shrine should be dated to this later pope's reign. What is interesting is that, behind the courtyard of the aedicula, the archaeologists found a room full of sarcophagi and, next to it, what seems to have been a baptistery. It is clear that the simple courtyard, with the aedicula as its focus, functioned not only as a church where the early Christians worshipped and received baptism, but also, just as the Liber Pontificalis states, as the burial ground where the first popes were laid to rest close to their founder.

The search for the bones of St Peter is surely one of the most fascinating archaeological stories of the 20th century. Not only was the project to dig beneath the massive basilica of St Peter's a precarious business, but the results were almost beyond belief or expectation. Who would have anticipated the discovery of a street of Roman mausolea leading to the very first church of St Peter's, dating from just a century after the apostle's martyrdom; and finally the recovery of the first pope's bones themselves.

On June 27 1968 a simple ceremony took place in the excavated space beneath St Peter's high altar. Pope Paul VI and a select band of archaeologists carefully placed plexiglass boxes containing Peter's remains back into the repository where they had been found by Ludwig Kaas in December 1950. Those few shattered relics belonging to Peter remain there today – a testimony to the remarkable tenacity of faith and tradition. The simple and romantic truth is that the church of Rome was built upon the very rock of Peter's bones.