Officials didn't wait for scientific evaluation before offering the relics up for public view; thousands waited for hours to catch a glimpse of the bones when they were displayed in Sofia, Bulgaria's capital.
Oxford professor Thomas Higham, whose lab subjected the bone fragments to radiocarbon dating and DNA sequencing, said he was skeptical at first.
"We didn't expect results that would be consistent with the expected - or hoped for - results of our Bulgarian colleagues," he said in a telephone interview. But he promised that the find, which has yet to be peer-reviewed, would stand up to scrutiny.
"We're very confident about the genetics," he said.
According to Christian tradition, John the Baptist foresaw the coming of Jesus and baptized him in the River Jordan. The ascetic desert-wandering prophet was later imprisoned and beheaded after criticizing the ruler of Galilee, Herod Anitpas.
Higham's Oxford colleague Georges Kazan, who has traced the tortured history of John the Baptist's remains, said it was possible that his relics could have ended up under the fourth-century monastery on St. Ivan's Island. (Ivan is the Slavic name for John.)
Nearby Constantinople - now known as Istanbul - was then at the center of the Christian world and the surrounding area was "full of monks and holy relics," he said. St. Ivan's Island, along an important Black Sea trade route, would have made sense as a place to store the saint's bones.
Then again, Kazan said he had identified more than 25 purported relics of John the Baptist scattered around the world, including 11 purporting to come from his head. Most appear to be bone fragments - i.e. part of a jaw - although some pieces are large enough that they're unlikely to be from the same person.
Higham said that, inevitably, some of the relics wouldn't stand up to scientific scrutiny.
"There are about eight or nine skulls of John the Baptist out there," he said. "They can't be all John the Baptist."
Higham's research was funded with a grant from National Geographic, whose channel is due to air a documentary on the find, titled Head of John the Baptist, on Sunday.