All but one child treated for gender dysphoria with puberty-blocking drugs at a leading NHS clinic also received cross-sex hormones, a study has shown.
The Tavistock and Portman Trust has argued the treatments are not linked.
The High Court ruled last week that under-16s are unlikely to be able to give informed consent to be treated with puberty-blocking drugs.
The trust said the study's findings were not accepted by a peer-reviewed journal until the day of the judgement.
These findings are from a study run by the Tavistock's Gender Identity Development Service (GIDS) - England's only NHS specialist gender clinic for children - and research partners at University College London Hospitals.
The study began in 2011 and enrolled 44 children aged between 12 and 15 over the following three years. At the time, only those aged 16 and over were eligible for puberty blockers in the UK.
When BBC Newsnight covered the study and its preliminary findings last year it highlighted how previous research suggested all young people who took blockers went on to take cross-sex hormones - the next stage towards transitioning to the opposite gender.
The Tavistock's newly published findings appear to confirm this, with 43 out of 44 participants - or 98% - choosing to start treatment with cross-sex hormones.
High court ruling
Earlier this month, the High Court ruled that children under-16 were unlikely to be able to give informed consent to treatment with puberty blockers.
The relationship between blockers and subsequent treatment with cross-sex hormones was a core feature of the case.
Lawyers representing the claimants said there was "a very high likelihood" children who start taking hormone blockers will later begin taking cross-sex hormones, leading potentially to infertility and impaired sexual function.
The Tavistock argued puberty blockers and cross-sex hormones were entirely separate stages of treatment and one does not automatically lead to the other.
The judges rejected that argument, saying "in our view this does not reflect the reality".
"The evidence shows that the vast majority of children who take [puberty blockers] move on to take cross-sex hormones," and that these are part of "one clinical pathway".
The study findings potentially lend further support to that assertion.
The Tavistock disputes this, saying that as those in this study had persistent and consistent gender dysphoria throughout their childhood, it is not surprising they would seek to continue treatment after 16.
It argues that the fact not all chose to do so shows this course of treatment is not an inevitability.
Furthermore, the data was requested by the High Court during the hearing, but the Tavistock did not provide it.
The data, the trust argued, would be published in a peer-reviewed journal, but comments were being reviewed by the study's principal investigator, Prof Russell Viner - the president of the Royal College of Paediatrics and Child Health.
However, the Tavistock published the data the day after the High Court handed down its judgement, and not in a peer-reviewed journal.
The Tavistock told the BBC that the paper was not accepted for publication until the day of the judgement and it was put into preprint that day.
The published study showed that treatment with the blocker brought about no change in psychological function.
This differs from Dutch findings "which reported improved psychological function," upon which many gender clinics have based their treatment.
Preliminary findings which showed that after a year on blockers, there was a significant increase in those answering the statement: "I deliberately try to hurt or kill myself", were not replicated across the duration of the study.
The study had no control group - with children who did not take puberty blockers - to enable the researchers to compare results with.
So, it is hard to infer cause and effect or draw conclusions as to the potential harms or benefits of this treatment.
The study also measured the impact of puberty blocking drugs on children's height and bone density.
The researchers found that suppressing puberty "reduced growth that was dependent on puberty hormones".
Height growth continued, "but more slowly than for their peers".
The Tavistock Trust said "the paper has now been accepted by a peer-reviewed journal and will be published soon".
All new referrals for puberty blockers are currently paused because of the High Court's ruling, and an NHS review into gender identity services for children and young people is currently under way.
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