"There was a discussion on questions of particular relevance for the Church in that country, such as the exercise of the rights to religious freedom, life and conscientious objection," it said in a statement.
President Obama and Pope Francis also agreed a "common commitment" to eradicate human trafficking during a historic first meeting and discussed immigration reform, the Vatican said.
They also underlined the need for international law to be respected in conflict zones around the world and for "a negotiated solution between the parties involved," the statement said.
In January, the pope issued his strongest condemnation yet of abortion, saying it was a sign of a "throwaway culture".
Although abortion is legal in Italy, access to the medical procedure can be extremely difficult for women.
Lives have also been risked after doctors refused to perform the procedure.
In 2010, an Italian woman was forced to have an abortion in a hospital toilet after allegedly being abandoned by doctors.