Addressing participants of a two-day conference in the Vatican on the evolving role of men and women according to Christian teachings, Francis said what he called "gender ideology" was a threat because it sought to erase the difference between the sexes.
"I have asked that studies be carried out into this ugly ideology of our times, which cancels out the differences and makes everything the same," the Pope said.
"Cancelling out the differences means cancelling out humanity."
Instead, man and woman are in a fruitful tension, the pontiff said.
Gender theory, often called gender ideology by its detractors, suggests that gender is more complex and fluid than the binary categories of male and female, and depends on more than visible sex characteristics.
The 87-year-old pontiff said he was still suffering from a recent cold and had asked an aide to read his speech but first wanted to "underline" his feelings on gender ideology.
He said he remembered reading a "prophetic" book called Lord of the World - a dystopian novel published in 1907 by a Catholic priest about a world where religion has no place - which warned of the risk of cancelling out differences between people.
"Read it if you have time, because it speaks of these problems of today," the Pope told his visitors.
with DPA