Although the chapel was named after Pope Clement VIII, it was designed with an altar by Pope St. Gregory the Great in about the year 600. This was because the original tomb of St. Peter, constructed by order of the Emperor Constantine, was missing an altar. Thus a proper chapel with a liturgical space was fashioned according to Pope Gregory's wishes around and above the Constantinian monument. One can only imagine the lavish liturgies that have taken place here over the centuries. The below image is what that original altar looked like, revealed here during work done in the late 1940s.
The present altar frontal design is new and was consecrated by Pius XII on June 5th in the Holy Year 1950. This was part of the inauguration of the new layout of the chapel and grottoes, with its lowered floor, after the tomb of Peter was excavated and his remains were re-discovered during the II World War excavations that were initiated by Pius XII and carried on through much of his pontificate. Those archeological excavations brought to light not only the tomb of the Apostle, but also the pagan necropolis from the first century located under the Basilica.
The chapel is today very well lit and was last renovated during the pontificate of Pius XII. It was cleaned in preparation for the Holy Year 2000 and has historically been open to the public in the morning hours from 7 am. The two side altars can be seen below.
| The side chapel on the right |
| The side chapel on the left |
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| 1950 - the new altar is consecrated after the renovations |
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| 1968 - the bones of St. Peter are put back in Peter's tomb |
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| Morning Mass in the chapel |
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| Rare image from a video of the previous altar before the new altar was installed in 1950 |











