So would it surprise you to know that every other day in Britain a baby is born looking different enough that doctors cannot instantly tell its sex? Would it make you feel less safe in your opinions if you knew that for 1 in 4,000 expectant parents a year, there is no answer to that first question: is it a boy or a girl? That almost certainly someone you know has started off his or her life like this? That, when you take into account the more subtle disorders of sexual differentiation, it becomes apparent only at puberty or later, as is the case for Semenya, and the rate doubles again? That children with physical problems such as this are one of medicine’s best-kept secrets?

Sit down and steady your nerves. Because after that first shock, there is another one. The outrage over Semenya has got British doctors angry. For it jeopardises one of the most progressive medical experiments of the 21st century. Very quietly, very delicately, the NHS has become world pioneers in this unexpected field. And what makes our team of specialist consultants so radical, when faced with a baby of ambiguous genitals, is how little they are doing to alter that, rather than how much.

Britain is the first to base treatment on the assumption that it should be acceptable for boys and girls to look far from “normal”. That doctors may be better off doing nothing to “fix” the kind of confusing genitals that incite laddish, locker-room bullying. This approach asks provocative questions of the rest of us. What makes us the sex we are, and what makes that so normal in the first place?

“These conditions are relatively common,” says Professor Adam Balen, consultant gynaecologist at Leeds General Infirmary. “I wouldn’t say they are hidden because that is an emotive term, but we’re obsessed by sex, and whenever sex is raised all of a sudden a prurient angle comes into it. We are not open enough in our society to discuss the variations that come with disorders of physical development.

“How do you define your gender? Is it defined by sex chromosomes? Not always. Is it your sex hormones? Not necessarily. Then what?”

Victorian doctors studied “hermaphrodites”, but that term is outlawed now, not only because of its offensive whiff of the circus freak but also because it is medically inaccurate (they have male and female genitalia, whereas often it is more complicated). Then, in the 1960s, the term “intersex” was coined. It’s still championed by some today despite unhelpful associations with “transsexual” (intersex conditions are biological rather than psychological — genetic or hormonal, or both).

It was at this point in the 1960s that a US doctor called John Money, when presented with a baby boy with a botched circumcision, decided to make “John” into a “Joan”. It was, as surgeons put it, simply easier to “make a hole rather than build a pole”.

Money’s experiment was fictionalised in the prize-winning bestseller Middlesex, by Jeffrey Eugenides. Money’s theory — that the child would develop a sexual identity that would fit whichever shape the surgeons fashioned its genitals into — was to dominate the world’s medical establishment for the rest of the 20th century. Until it was challenged by UK doctors.

When Sophia, 45, from Brighton, was born with a genetic condition (called 5-ARD) that made her sex initially unclear, her parents were told nothing. This secrecy by the medical teams was absolutely standard. “They didn’t know what I was, but all they said to my parents was, ‘there’s a problem, we’re doing some kind of repair’.”

She was sent home to an almost impossible life. Her parents were told she was a boy, but they “picked up something strange was going on”. Meanwhile the botched “repair” made life as a boy utterly miserable.

In adulthood Sophia now lives (“exists” is the word she uses) as a woman, campaigning passionately against surgery to “normalise” babies. Wouldn’t it be kinder, I ask, to make a child less different in the eyes of their peers, to spare the taunts? “That argument is countered by the messiness the surgery itself causes,” she says.

Laurence Rangecroft, a recently retired consultant paediatrician who specialised in these cases at the Royal Victoria Infirmary in Newcastle, remembers the days of the hush-hush operations. “Surgeons used to think, ‘There’s a problem, we need to correct it’, and that’s what they, with the best of intentions, enthusiastically set out to do. But with any operation that is complicated and difficult to perform, you’re not always going to get good results.”

Then, in 1997, Money’s star patient, “Joan” went public with his story. Not only had he reverted to his male identity as soon as he could, but his life had been blighted by Money’s treatment. His male twin had died of an overdose, and he himself committed suicide in 2004.

“In the US, surgeons got very scared,” Rangecroft says. Corrective surgery looked risky, but so did the alternative. “With fears of litigation, with either course of action, I had one surgeon say to me, ‘It’s reached a state of paralysis, people don’t know what is the right thing to do any more’.”

Enter Sarah Creighton. As a gynaecologist at University College Hospital, she was the first to set out to compare those whose doctors had, at birth, attempted to “normalise” their genitals, and those who had no surgery. Nobody had followed up on patients in the past, as, cloaked in secrecy, doctors had concealed the truth from parents and child.

But she tracked them down and her groundbreaking study in The Lancet found that those who were left as nature made them fared as well, if not better, than those who had been normalised. Being yourself was more important than being like others.

Take Gordon, a man who lives on the north coast of Britain, who “was a male child with ambiguous genitals”. Unusually for his time, he escaped surgery. He was raised as a girl until the age of 3, because of a genetic condition that drastically lowers testosterone levels. Then he was brought up, unhappily, because of changing-room bullying, as a boy. “I always had this idea that I had sisters that I was detached from. It has occurred to me that, since I was dressed as a girl as a baby, I was feeling detached from myself.” His condition was diagnosed and treated only in his middle age, after a lifetime of struggling to succeed in a macho family, school and workplace — never “feeling or acting right”. “Typical males would consider me a sad specimen. But my girlfriend thinks it’s great.”

So, on reflection, he is glad he was not “corrected” at birth. “I see a society that doesn’t want to admit variation exists.”

Creighton’s findings were to start a British-led revolution: first, telling parents the truth about their child’s ambiguous-looking sex and, even more radical, saying that perhaps he or she could stay that way. Creighton backs the statistic from the Scottish study: that one baby in 4,000 is sexually ambiguous at birth. “It is difficult, as the first question any couple ask at birth is, ‘what have we got?’” she says.

Now, instead of paternalistic bluster, the doctor is trained to reply, “We’re not sure yet”, and refer to one of the major centres — University College Hospital, London, for the South of England; Balen’s team in Leeds for the North — for a battery of tests and genetic analysis.

This is a shocking time for parents — a 2006 survey by the Scottish Audit of Genital Anomalies found that 95 per cent of parents were desperate for more information on the condition after the birth. Most were extremely worried about “ridicule and stigma” for their baby and the difficulty of discussing it with friends or relatives.

“It can take days or weeks to determine the sex — the limit on naming a child is six weeks and sometimes that has to be extended,” Creighton says.

What about relatives, clamouring to know the baby’s name?

“We advise parents to say the baby’s poorly, they are awaiting tests. All children are then allocated boy or girl, but much more controversial is: do you proceed to surgery? That is hard to undo. We tend to think that surgery is all-powerful and by having surgery you have a cure. These aren’t conditions that you can cure.”

So for the past ten years British parents have been discouraged from surgery purely for reasons of social acceptability, thereby allowing the child a decision when they are older. It’s not always easy. One surgeon said the parents of a genetic girl, with an enlarged clitoris, were begging him for surgery, “rather than the other way around”. Creighton says that the risks have to be carefully explained — surgery will affect any future sex life, for example.

“We are leaders in this field, worldwide, in terms of disclosure to the parents and child, and challenging surgery,” she says.

So a generation of children, now coming up to puberty, are facing their own choice about whether they want to look like a normal man or woman, or remain as something far more unusual. They are pioneers.

“It is now as adolescents that they are getting the full information. It’s a stormy time for all teenagers, but it’s really difficult for them,” Creighton says.

Everyone I talk to believes that the new strategy is right, after many decades of getting it wrong. But it is uncharted waters. A few years from now the first of the new generation will be able to tell their own story. Are we ready for what they will say?

At the end of the novel Middlesex, the mother of the hero tells her it would have been easier to hide her condition, remain the way she was. “This is the way I was,” is the hero’s reply. When I ask Sophia, in my blundering way, which sex she is, genetically, she replies: “Genetically, I am me.”

When the sex changes

Three years ago Santhi Soundarajan, the Indian athlete, was stripped of a silver medal at the Asian Games after failing a sex test. Later the 25-year-old was reported to have attempted suicide, although she denied the claim. She has since set up her own youth sports academy. “A test cannot take away from you who you are,” she said.

Erika Schinegger was preparing for the 1968 Winter Olympics when a routine medical test determined that the Austrian skiing champion was chromosomally male. He was disqualified. For Schinegger, the tests confirmed doubts that had plagued him since puberty, and soon Erika became Erik. He continued to ski, but has spoken of his feelings of isolation and depression during the process of alteration. “Not one team mate visited me during the six months that I was in hospital undergoing the operations. The federation didn’t allow it. A lot of people ran away, best friends included.”

Fiore de Henriquez, the Italian sculptress, was brought up as a girl but during her teens, as she began to menstruate and develop breasts, she discovered that she also had male genitalia. She lived as a woman and only revealed her secret near the end of her life. “My mother used to call me a monster,” she said. “But I didn’t feel like a monster.”

She was the hard-drinking, cros — dressing, gun-toting frontier cowgirl — and some scholars believe that Martha Jane Canary-Burke, better known as Calamity Jane, was “intersex”. But the rumour has never been proved and as she had two children, other historians say it is unlikely.

As a child, the writer Lady Colin Campbell preferred to play with dolls but her malformed genitalia persuaded her parents to raise her as a boy named George. She describes puberty as “like a glimpse into the bowels of Hell”. At 21 she had corrective surgery and officially became Georgia.