John Swinney has praised a landmark report into gender identity services for young people as "substantial" and "evidence-based".
The new SNP leader said the Cass review must be taken "extremely seriously".
It comes after SNP ministers were accused of playing down the report when the Greens were part of the Government.
The Greens' scepticism is believed to have hastened their sacking from the Government.
Dr Hilary Cass's review looked at gender identity services for under-18s in NHS England.
It found gender medicine to be operating on "shaky foundations" when it came to the evidence for medical treatment like prescribing hormones to pause puberty or to transition to the opposite sex.
When asked if he accepted the findings of the review and whether he would implement its recommendations, Swinney said: "I think the Cass review has got to be taken extremely seriously.
"It's a substantial evidence-based proposal. It's been considered by government and also by clinicians.
"Crucially for me, clinical opinion is essential on these questions.
“The Government will take a rational evidence based approach to the consideration of the Cass Review, drawing on the evidence put to us by clinicians.
“On matters of such sensitivity about the wellbeing of children and young people we should listen to clinicians.”
NHS Greater Glasgow and Clyde and NHS Lothian last month confirmed a pause on new prescriptions for puberty hormone suppressants for young people with gender dysphoria.
Scottish politics
NHS Scotland is reviewing gender services for both adults and children. New protocols for adults have been delayed but are expected to be published before the summer.
Swinney was speaking at Glasgow University as he accepted the role of SNP leader for the second time.
He is expected to become first minister later this week.
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