The male skeleton was found in a suburb of Prague and is buried in a manner previously only seen for female burials.
The body is believed to date from between 2900 and 2500BC and is from the Corded Ware culture of the Copper Age.
Men’s bodies from that age and culture are usually found buried with their heads towards the west and with weapons.
But this skeleton was found with its head towards the east and was surrounded by domestic jugs – as women’s bodies from the time are usually found.
At a press conference in Prague yesterday, archaeologists theorised that the person may have been transgender or ‘third sex’.
Kamila Remišová, the head of the research team, said: “From history and ethnology, we know that when a culture had strict burial rules they never made mistakes with these sort of things.”