Pope Francis has criticised the teaching gender theory in schools, calling it "insidious indoctrination". The head of the Christian Church told the press on board the papal flight that while he was respectful of the homosexual and transgender communities, he was against the idea of children being taught about choosing gender identities different from their biological ones.

"It is one thing for a person to have this tendency, this option, and even change sex," he said. "But it is another thing to teach it, gender theory, in schools along these lines in order to change mentality. I call this ideological colonisation," Francis added during his flight back from a visit to Georgia and Azerbaijan.

"When a person (who is gay) arrives before Jesus, Jesus certainly will not say, 'Go away because you are homosexual,'" the pontiff said, recounting a story about a Spanish individual who transitioned into a man and then married a woman. After the local church told the couple they would "go to hell" for their actions, they wrote to the Pope seeking advice and he received them and treated them respectfully.

"Life is life, and things should be taken as they come," said the pontiff, who once famously asked "who am I to judge?" when questioned about homosexuality.

"Please don't write that the pope will sanctify transsexuals. I can see the front pages of papers now," he added on a lighter note. "It is a moral question, and it must be resolved as best as possible, always with the mercy of God."

During his Caucasus visit, Francis told priests and nuns that teaching gender theory in schools was part of a "global war" against marriage. However, in Azerbaijan he focused more on religious tolerance and commended the country, which has the second largest Shia Muslim population in the world, for living harmoniously despite the religious differences of its citizens.

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"From this highly symbolic place, a heartfelt cry rises up once again: No more violence in the name of God!" he said during a visit to the country's main mosque in the capital Baku. "May his most holy name be adored, not profaned or bartered as a commodity through forms of hatred and human opposition."

While speaking with President Ilham Aliyev and government officials he added, "These good relations assume great significance for peaceful coexistence and for peace in the world. They demonstrate that among followers of different religious confessions, cordial relations, respect and cooperation for the common good are possible."

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