Great Ormond Street Hospital is not meeting care standards for intersex children, a BBC investigation says.
It found that some patients who had been born with sexual development disorders, and their families, had no access to psychological care.
And not all cases were properly discussed before the patient had life changing, irreversible surgery.
Health regulator CQC is making inquiries. The hospital said it was committed to working with seriously ill children.
Intersex, also known as disorders of sexual development (DSD), is when sex characteristics - including genitals, reproductive organs and chromosome patterns - do not fit into the typical notions of female or male bodies.
The BBC has learned that at Great Ormond Street Hospital (GOSH):
- There is currently no face-to-face psychological support for children and their families who have been referred in the last six months despite surgery continuing. The BBC understands tens of families are waiting for therapy. For several years not all children and their families have had access to face-to-face support, before having surgery
- Not all cases were discussed at full the multidisciplinary team meetings at GOSH
- Information about this surgery is complex but information given to parents is not in a written form that they can take away, to ensure proper comprehension prior to giving informed consent for surgery. The BBC has been told that this raises doubts as to whether parents have given truly informed consent on behalf of their child before irreversible surgery.
Over the last decade, standards and guidelines say DSD cases should be discussed by specialist teams of experts, to ensure the best possible outcome. They also say that it is crucial that families and children should be seen by a psychologist.
Prof Ieuan Hughes, emeritus professor of paediatrics at the University of Cambridge and an expert in hormone disorders told the BBC that DSD was a "very complicated area of medicine".
He said it was vital families got support from a psychologist prior to making decisions about surgery, so parents were fully aware of the life long-implications on children.
When asked by the BBC if surgery should continue in hospitals not meeting the national standards, Prof Hughes said: "It seems reasonable to me to just take a pause, get the problem sorted and get back on track as soon as possible."
'I went to bed a boy and woke up a girl'
When Joe Holliday was born in 1988 it was not clear if he was a boy or a girl.
During development in the womb his genitals did not fully form and he was born with a large hole in his abdomen.
The 29-year-old says specialists at Great Ormond Street Hospital told his mother he would be better being a girl, because it was easier surgically and he would not handle being a man without male genitalia.
On Joe's first birthday, his mother put him to bed and the next day brought him up as Joella. As advised by the medical team, she changed all his clothes from blue to pink overnight.
He featured in a BBC documentary in 1998, when he was 10 years old, which followed his family's legal fight to get him recognised as a girl on his birth certificate.
But from 10 years old onward, Joella suffered with depression and anxiety. He self-harmed and attempted suicide.
"I had years of feeling like I was in a black hole and not knowing why," he told the BBC.
In his 20s, by chance, he saw his medical notes and read that blood tests had shown his chromosomes to be XY - genetically male.
He also learned his testes had been removed when he was eighteen months old, despite being perfectly healthy, he said.
"I felt I feel like I lost such a large part of my life - 15 years of my life that I spent depressed and almost a recluse at one point," he said.
At the time, the decision over raising Joe as a Joella, was considered to be best practice, but now most children now born with this condition are raised as male.
He said that although the advice was different when he had his surgery 30 years ago, it was "not acceptable" that patients were not being supported now.
Experts have told the BBC that Great Ormond Street Hospital for Children NHS Foundation trust is seen as the leading hospital for care for these children and regional centres refer in for specialist opinions of the multi-disciplinary team.
In a statement the hospital said that patients diagnosed at GOSH were discussed and treatment decisions were taken through these multi-disciplinary teams.
A specialist psychologist is due to start at the hospital "in the coming weeks", the trust said, but it would not comment on whether the post had been filled.
The trust declined to comment on the other concerns the BBC uncovered, on whether children referred from other hospitals for specialist opinion benefitted from input from their specialist team at GOSH prior to surgery and on whether it was meeting national standards.
What is intersex?
- There are many congenital variations of disorders of sex development
- Some traits are visible at birth, others not until puberty and some variations in chromosomes may not be physically apparent at all
- Worldwide, between 0.05% and 1.7% of people have intersex traits, according to the Office of the United Nations High Commissioner of Human rights
An NHS England spokesperson said: "Disorders of sexual development (DSD) are rare and complex, but it is right that children and their families should be appropriately involved in decisions about their care."
Professor Ted Baker, the chief inspector of hospitals at the Care Quality Commission said: "We have asked Great Ormond Street Hospital to provide further information about the concerns, which were brought to our attention by the BBC."
He added: "We are clear that NHS trusts and all providers of health and social care must have regard for nationally recognised guidance about delivering safe care and treatment."
The CQC has currently rated the surgical department at Great Ormond Street Hospital for Children NHS Foundation Trust as requiring improvement.
Dr Faye Kirkland is a reporter for the BBC but also a working GP
Clarification 19 October 2017: This article has been amended to clarify that the CQC has made inquiries following up on information of concern prior to a possible inspection. The headline has also been amended.