The Vatican: Photos Reveal What's Beneath St. Peter's

March 1, 2013 1:11 PM EST

The walled, pint-sized city-state known as the Vatican physically takes up around 100 acres in the center of Rome, but occupies a vast, measureless space in the lives of more than a billion practicing Catholics around the globe. Over the past few years, of course, the goings on in the holy enclave have also grabbed a lot of real estate in the world’s media, as Pope Benedict XVI — the 265th successor of Saint Peter — abruptly resigned as head of the faith and Pope Francis was installed.

Here, as the most recent pope continues to puts his personal stamp on the ancient role — and appears willing to make the entire Vatican more open to the faithful — LIFE.com looks back more than six decades to a time when the church was actively unearthing its own secrets . . . literally.

In 1950, LIFE reported on a years-long effort undertaken beneath the staggeringly ornate public realms of the Vatican, as teams of workers meticulously excavated the myriad tombs and other long-sealed, centuries-old chambers far underground. Nat Farbman’s color and black and white images in this gallery — most of which never ran in LIFE — were touted on the cover of the March 27, 1950, issue of the magazine as “exclusive pictures” for the story titled “The Search for the Bones of St. Peter.”

Deep in the earth below the great basilica of St. Peter’s in Rome [LIFE wrote] the clink of pickaxes and the scrape of shovels in the hands of workmen have been echoing dimly for 10 years. In the utmost secrecy, they have penetrated into a pagan cemetery buried for 16 centuries. Architects feared they might disturb the foundations on which rests the world’s largest church. But the workmen, with careful hands, pushed forward finally to the area where, according to a basic tenet of the Catholic Church, the bones of St. Peter were buried about A.D. 66.

The Church has always held that Peter was buried in a pagan cemetery on Vatican Hill. Now, for the first time, there is archaeological evidence to support this: the newly discovered tombs, which LIFE shows [in these exclusive pictures].

The greatest secret of all — whether the relics of the Chief Apostle himself were actually found — is one which the Vatican reserves for itself, although there have been rumors that the discovery of the relics will be announced at an appropriate time during the Holy Year.

In the end, LIFE’s editors expressed their appreciation for “the privilege of guiding LIFE’s readers through these chambers where in the dust of antiquity can be traced the humble yet transcendent beginnings of the Christian faith.”

[MORE: Buy the LIFE book, Pope Francis: The Vicar of Christ, From Saint Peter to Today.]

NOTE: In December 1950 Pope Pius XII announced that bones discovered during the excavation could not conclusively be said to be Peter’s. Two decades later, in 1968, Pope Paul VI announced that other bones unearthed beneath the basilica — discovered in a marble-lined repository, covered with a gold and purple cloth and belonging to a man around 5′ 6″ tall who had likely died between the ages of 65 and 70 — were, in the judgment of “the talented and prudent people” in charge of the dig, indeed St. Peter’s.

To this day, of course, that claim has as many doubters as adherents.

Liz Ronk, who edited this gallery, is the Photo Editor for LIFE.com. Follow her on Twitter at @LizabethRonk.