Findings from the study, run by the Tavistock and Portman NHS Trust's Gender Identity Development Service (GIDS), England's only NHS specialist gender clinic for children, and research partners at University College London Hospitals, could raise questions over a recent High Court judgment on the use of puberty blocker for under-16s.
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.
It found that of the 44 children who took part, 43 received cross-sex hormones after taking puberty blockers.
The NHS trust argues that the treatments are not “inextricably linked” but said “it is not surprising they would seek to continue treatment after 16”.
The study was published after the High Court ruled that children under 16 are unlikely to be able to give informed consent to undergo treatment with puberty-blocking drugs.
Delivering the ruling in the case against the trust earlier this month, Dame Victoria Sharp, sitting with Lord Justice Lewis and Mrs Justice Lieven, said: "It is highly unlikely that a child aged 13 or under would be competent to give consent to the administration of puberty blockers.
"It is doubtful that a child aged 14 or 15 could understand and weigh the long-term risks and consequences of the administration of puberty blockers."
The case was brought by Kiera Bell, a 23-year-old woman who was referred to the Tavistock Centre as a teenager and was prescribed puberty blockers aged 16.
She argued the clinic should have challenged her more over her decision to transition to a male as a teenager.
A second claim was brought by the mother of an unnamed 15-year-old girl with autism, who is awaiting treatment at the clinic.
The new study was published the day after the High Court handed down its judgment.
It shows no change in psychological function in young people who used puberty blockers.
It also measured the impact of puberty blocking drugs on children's height and bone density.
Researchers found that suppressing puberty "reduced growth that was dependent on puberty hormones", however, height growth continued, "but more slowly than for their peers".
Tavistock and Portman NHS Trust has been contacted for further comment.
