The two leaders met at the Vatican's apostolic palace where the pontiff offered Obama a copy of a document titled "An Instruction on Certain Bioethical Questions", according to CNN.
While Obama supports abortion rights and funding embryonic stem cell research, the Vatican is staunchly opposed to both. In a paper that was released in December, the Vatican hardened its opposition to using embryos for stem cell research and affirmed the dignity of every human life – beginning at conception.
During Friday's private discussion that lasted about 40 minutes, Obama reaffirmed his personal commitment to try to reduce the number of abortions in the United States, according to Vatican spokesman the Rev Federico Lombardi.
Earlier this year at a highly publicised commencement at the University of Notre Dame, Obama conceded that the views of the pro-life and pro-choice camps are "irreconcilable" and that each side will continue to make its case.
But the President pressed for civil debate and urged a search for "common ground".
As they ended their meeting, President Obama told Pope Benedict that he looks forward to "a very strong relationship."
Earlier, White House spokesman Robert Gibbs said that even though the pope and Obama may not agree on everything, "there are steps that can be taken ... that will show progress, whether it's on something like unintended pregnancy or adoption".
After taking office in January, Obama ended the Bush administration's ban on funding international groups that perform or promote abortions and also reversed a ban on federal funding of embryonic stem cell research.
