The woman's skull was revealed among other bones after a tractor wheel broke through the roof of a neolithic burial chamber.
The discovery has set Martin Pepler digging into his family history and the unusual condition known as "step head". The Orkney tomb is featured tonight on the BBC2 programme Meet the Ancestors. Many skulls from the period have been uncovered in the islands, but none has the sort of large bony lump found on the woman's head.
The Museum of London has a skull with a similar bump from the 17th century, when as much as 10 per cent of the capital's population had stepped heads, but the programme makers could find no-one with the condition living today.
Then, by chance, 53-year-old Mr Pepler, who is based in London, visited the museum.
"I have an extra ridge of bone on the back of my head which gives it a shape a little like a German helmet. When I was a child, I never wanted to get my hair cut short because I was afraid I'd get teased. But when I visited the museum, I thought, 'My God, that's like my skull'," he said.
His father, Albert Pepler, who died in 1974, had an even more pronounced lump. "He always used to say it was because we were old Londoners." Mr Pepler intends to trace the family tree to see if it can shed any light on the Orcadian connection. The presenter tonight, Julian Richards, hopes the programme will spark a scientific study into step head.
After the unusual skull and other remains were removed from the Orkney tomb last year, a narrow slot was found in the burial chamber's carefully crafted stone walls.
It was the first "light box" discovered at a Stone Age tomb in the British Isles and archaeologists believe its purpose was to allow sunlight to shine on the bones twice a year. Earlier this week, it was claimed a man with a deformed skull and five children whose 4,000-year-old bones were found on a building site in central Scotland, may have been sacrificial offerings to an earth goddess.
Nobody can actually prove how the odd group in the ancient stone coffin met their death, but archaeologists who have studied the bones for the past 15 months believe ritual sacrifice could be a strong possibility.