At 11, Matilda liked to be known as Matt and referred to as he, but at home with her family she was Tilds. Born a girl, Matilda wore her hair short and dressed in boys’ clothes. She is autistic and talks little, but in copious notebooks depicted herself as male. As puberty loomed, so did a hard question: was Matilda transgender?

Matt, as he is now, is one of two children featured in a new documentary about the Tavistock and Portman NHS Trust, the only centre in England specialising in child gender identity. The other child, Ash – born a boy but who has unwaveringly identified as a girl since she was three – seems clear-cut. But Matt’s case is more typical of the complex questions at the heart of the controversial trans debate, which is increasingly ending up on newspaper front pages, or in court.

In the last month, a seven-year-old boy was removed from his mother by a judge who ruled he was being brought up as a girl against his will, while the parents of a 14-year-old girl condemned social workers for pressing their daughter to “socially transition” (ie take a male name and pronouns) without their consent when they believe she has wider mental health problems. Meanwhile, the children’s TV channel CBBC has been accused of confusing young viewers with its online programme Just a Girl, about how Ben became Amy.

Ten years ago, the Tavistock received 40 referrals a year; now it is 1,400. Boys were once the majority – now around 1,000 of its patients are girls. Undoubtedly, trans children, who in previous generations suffered trauma and discrimination silently or even killed themselves, are now coming forward for treatment.

Matt, aged 11, was born female but identifies as male

Yet this surge throws up other questions. Is gender confusion sometimes another manifestation of teenage anxiety, such as anorexia or self harm? Are some girls who reject a rigid, commercialised “femininity” of pink, princesses and make-up parties led to feel they may be boys? Are we observing, to some extent, an online-generated trend?

Dr Bernadette Wren, head of psychology at the Tavistock, doesn’t claim to know all the answers. The field of gender identity is so new and fast evolving, she says, “I just have to be really honest and say at the moment we don’t have a way of understanding it completely.”

Previously more boys were referred, “because if you’re a boy who likes girls’ stuff people pay attention to that, in a way that we’ve never done with tomboys”. So is being a “butch” woman less culturally acceptable now? Certainly some girls they see came out as lesbians, says Dr Wren, then later started to question their gender.

“But we won’t just assume, ‘Oh my goodness, you don’t like your breasts. You’re trans.’” Rather, the Tavistock tries to unpick a child’s unhappiness, “because we are aware that puberty is a very stressful time for everybody. There is such a pressure to look right, look gorgeous, that for young people being reasonably happy in your body is the exception now, rather than the rule.”

Dr Wren’s caution reflects the difficult position of gender experts. In North America, trans activists have attacked a “wait and see” attitude to children as dangerous and akin to the “conversion therapy” once used to try to make gay men straight. A Canadian clinic, led by a psychologist who believed young children should initially be encouraged to feel comfortable in their natal bodies, was closed down. In treating children, Dr Wren believes in “maintaining a degree of uncertainty about what the future might be and keeping the options open.” But the difficulty is remaining open-minded while ensuring support for the tiny number of highly vulnerable children who will definitely transition, “because it’s not obvious who they are when they are only four or five”.

Ash, aged 8, was born male but identifies as female

But the Tavistock’s caution can be unpopular with parents who crave a quick fix for a deeply troubled child. A new type of parent is emerging who, after some online research, is self-diagnosing their child as trans on superficial evidence.

A recent edition of the Radio 4 programme iPM featured a girl called Leo whose mother believed she was a boy because she liked Wolverine and wanted a pirate-themed birthday party, assumptions unchallenged by presenter Jennifer Tracey. Dr Wren says several Tavistock clinicians complained to the BBC: “There was concern about it. 

Moreover, as High Court judge Mr Justice Hayden said as he removed the seven-year-old from his mother, “an emerging orthodoxy” about trans identity had prevented social workers from intervening despite the mother’s aggression and evidence of neglect. Professionals fear not just being labelled bigots “on the wrong side of history” but of breaching the Equality Act, which enshrines trans rights. 

The Tavistock encourages children to explore and experiment, wearing any clothes they like, rejecting stereotypes: “We say take a doll to school on toy day if you’re a boy. The school has to learn to tolerate it.”

Early social transition, they believe, can create a false impression: children start to believe growing up as the opposite gender will automatically follow putting on a dress and changing a name. “When, actually, we know it requires a lot of hard work and medical intervention to change the body,” says Dr Wren. “That’s not to be negative about it, because people go through it and have great lives. But the child might think, ‘Well, I’m growing up as a girl, aren’t I?” And you don’t want to shatter that and explain vaginoplasty to a six-year-old.”

In the Channel 4 documentary, Ash, the trans girl, says she can feel her burgeoning breasts: her distressed mother, unable to lie, doesn’t know what to say.

At around 11 or 12, children will be considered for “blockers” to halt puberty, which can be a hugely traumatic time for children who are unsure about their gender.

These drugs are reversible, a “pause button” so a child has more time to work out their identity before breasts grow or voices drop, which will make it harder to “pass” as the opposite gender as adults. But in practice, almost all children who take blockers proceed to cross-gender hormones. (At 18, they can then join a waiting list for surgery.)

The Tavistock, under an NHS protocol, does not prescribe hormones until a child is 16. This delays the opposite-sex puberty some long for. These years in Peter Pan limbo can be hugely frustrating, and parents may resort to private clinics that prescribe hormones at 12.

But Dr Wren believes this wait is a vital safeguard: hormones must be taken for life and destroy fertility. Does she worry about setting an 11-year-old on such a course? “We all worry,” she says with feeling. “Of course we worry.”

But, she argues, in all fields of medicine, a doctor-knows-best paternalism is outdated: patients want responsibility for their own choices. And, meanwhile, the growth of plastic surgery creates the impression that our bodies can be moulded to fit our visions of ourselves. 

“When I talk to trans activists, they feel really strongly about this,” says Dr Wren. “They say in the modern world, people make their own mistakes. Now that’s quite tough on an 11-year old.”

Kids on the edge: the Gender Clinic is on tonight at 10pm on Channel 4