There's no word yet on what the two discussed, but ahead of the meeting, Khatami told a conference in Rome that the wounds between Christians and Muslims were still "very deep."
He said one meeting with the pope was not enough to heal all those wounds, but said it was at least a joint effort to start the process.
In a speech in September, Pope Benedict quoted a 14th-century Byzantine emperor as saying Islam had only brought evil to the world and that it was spread by the sword.
Today's meeting was Khatami's second with a pope, following an audience with the late Pope John Paul II in 1999, two years after Khatami took office.
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