The document issued on Monday, during LGBT pride month, is the Vatican's first on gender theory.
In it, the Vatican also insists on the sexual complementary of men and women.
LGBT Catholics immediately denounced it as harmful and contributing to hatred, bigotry and violence against gay and transgender people.
Advocacy group New Ways Ministry said it will confuse people who are struggling with questions about gender identity and sexual orientation.
The text, Male And Female He Created Them, was issued by the Congregation for Catholic Education, which said it was intended to help Catholic teachers, parents, students and clergy address the "educational crisis" in the field of teaching sexuality.
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