Keyes and 20 others were charged with trespassing, Dennis Brown, a spokesman for the Catholic university, said. Brown said the university has a long-standing policy that only student-led demonstrations are allowed on campus with approval from the office of student affairs.
Notre Dame invited Obama to deliver the commencement address and receive an honorary degree May 17, causing an uproar because of his support of abortion rights. Many of the protesters Friday pushed baby strollers covered in fake blood.
Operation Rescue described the demonstration as peaceful.
"Notre Dame arrests Christians who defend babies, and honors a man who kills them," Randall Terry, the group's founder, said. "This is an open wound in the Church. The question is this: Will a Catholic Bishop step up and demand this betrayal of the Faith be brought to a halt?"
Obama will be the sixth U.S. president to deliver the commencement address at Notre Dame and the ninth to receive an honorary degree. Notre Dame President Father John Jenkins said in March presidents from both major parties have spoken to Notre Dame graduating classes.
"They've given important addresses on international affairs, human rights, service, and we're delighted that President Obama is continuing that tradition," he said.
Keyes has run for the Republican nomination for president several times. In 2008, he won 2.7 percent of the primary vote in North Carolina, his best showing.
He was the Republican candidate against Obama in Illinois in 2004, winning 27 percent of the vote.
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