Tests have revealed Caster Semenya's testosterone level to be three times higher than those normally expected in a female sample, BBC Sport understands.
Analysis prior to the World Athletics Championships coupled with her rapid improvement prompted calls for a gender test from the sport's governing body.
News of the test was made public just hours before the 18-year-old South African won 800m gold in Berlin.
A high level of testosterone does not always equate to a failed drugs test.
But the news will only increase speculation surrounding Semenya, who arrived back in South Africa to a rapturous welcome on Tuesday.
Semenya was welcomed by hundreds of well-wishers on her return to South Africa
Hundreds turned out in Johannesburg to greet the teenager, who has stunned the athletics world with her performances this season.
She ran a time of one minute, 56.72 seconds in Bambous in July to smash her previous personal best by more than seven seconds.
She also broke Zola Budd's long-standing South African record and arrived at the World Championships as the newly crowned African junior champion.
Then in Berlin she left her rivals trailing to win gold in a time of 1:55.45.
Janeth Jepkosgei was second, a massive 2.45 seconds adrift, with Britain's Jenny Meadows taking the bronze medal.
Only hours before the race, it leaked out that the International Association of Athletics Federations (IAAF) had demanded Semenya take a gender test amid fears she should not be allowed to run as a woman.
It has since emerged that news of the test only became public knowledge because a fax was sent to the wrong person.
Caster is like my child. I know where she comes from. For myself, I know Caster is a girl
Semenya's uncle
It has also been revealed that following the findings of initial tests, the South Africans were asked by the IAAF to withdraw her from the team at the World Championships.
Since then, both her family and South African athletics chiefs have leapt to her defence, insisting she is 100% female.
"Caster is a girl. I am not worried about that too much," said her uncle on her arrival back in South Africa.
"Caster is like my child. I know where she comes from. For myself, I know Caster is a girl."
Leonard Chuene, president of Athletics South Africa (ASA), has resigned from his seat on the IAAF board in protest against the organisation's treatment of Semenya.
"It will not be fair for me to attack the IAAF as a council member and representative of South Africa. It is a conflict of interest," Chuene told BBC's Newshour programme.
Chuene also asked that the issue be laid to rest.
"We have not once, as ASA, doubted her," he said. "It's very simple - she's a girl.
"We took this child to Poland to the junior championship under the IAAF. Why was there no story about it? She was accepted there.
"No-one said anything there because she did not do anything special. She is the same girl."
Semenya has been humiliated - Holmes
Testosterone levels can vary widely, which makes it hard to detect possible infractions.
When analysis shows an athlete to have a raised level, they are monitored at regular intervals over a set period to establish what their underlying levels would be.
That is then used as a marker for the future, so any sharp differences immediately stand out as suspicious.
An analysis of Semenya's testosterone levels was carried out in South Africa and it is understood that this information contributed to the IAAF's decision to request the ASA carry out a detailed "gender verification" test on the athlete.
Those medical tests are said to be ongoing, with the results not expected for several weeks.
On Sunday, IAAF president Lamine Diack admitted the affair could have been treated with more sensitivity.
"It should not even have become an issue if the confidentiality had been respected," he said. "There was a leak of confidentiality at some point and this led to some insensitive reactions."
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