Francis opposes same-sex marriage and abortion, which isn't surprising as leader of the socially conservative Catholic church.
But as a cardinal, Francis clashed with the government of Argentine President Cristina Fernandez de Kirchner over his opposition to gay marriage and free distribution of contraceptives.
His career as a priest in Argentina coincided with the so-called Dirty War -- and some say the church didn't do enough to confront the military dictatorship.
As many as 30,000 people died or disappeared during the seven-year period that began with a coup in 1976.
Francis, in particular, was accused in a complaint of complicity in the 1976 kidnapping of two liberal Jesuit priests, Allen wrote. Francis denied the charge.
"The best evidence that I know of that this was all a lie and a series of salacious attacks was that Amnesty International who investigated that said that was all untrue," said Jim Nicholson, former U.S. Ambassador to the Holy See. "These were unfair accusations of this fine priest."
But Amnesty International said it did not investigate any individual for their specific involvement.
"Our research focused on the plight of the disappeared," said Susanna Flood, media director for Amnesty International.
5. He faces a host of challenges ahead
Francis takes the helm of a church that has been rocked in recent years by sex abuse by priests and claims of corruption and infighting among the church hierarchy.
He may need to find a way to draw new Catholics into the church where it is in decline, said Phillip M. Thompson, executive director of the Aquinas Center of Theology at Emory University.
And he'll also need to find ways of working with shifting viewpoints among Catholics. In the United States, for example, 90% of Catholics are using contraception and 82% think it is morally permissible.
"The church has conservative positions on human sexuality, bioethics, etc., but liberal positions on issues such as economic regulation, the death penalty and immigration," Thompson said. "A church divided against itself seems unlikely to renew our political or cultural structures."