Obama then presented the pope with a seed chest with fruit and vegetable seeds used in the White House Garden, in honor of the pope's announcement earlier this year that he's opening the gardens of the papal summer residence to the public.
The chest was custom-made of leather and reclaimed wood from the Baltimore Basilica, one of the oldest Catholic cathedrals in the U.S, and inscribed with the date of their meeting.
As they meet, the six-year president, with his sinking poll numbers, would not be blamed for seeking some reflected glory from a pope who, one year into his pontificate, is viewed as an agent of change in the Roman Catholic Church.
Obama is the ninth president to make an official visit to the Vatican.
His audience marks a change of pace for the president, who has devoted the past three days of a weeklong, four-country trip to securing European unity against Russia's aggressive posture toward Ukraine.
The pope whom Obama will sit with this time is a different pontiff than the last one to host him.
Obama visited Pope Benedict XVI in 2009, a cordial meeting that nevertheless drew attention to the differences between the church and Obama on abortion.