In a statement well before the ceremony, Jenkins wrote that the invitation "does not mean we support all of his positions … [on] abortion and embryonic stem cell research."
White House officials had said in advance that the president would address the protests in his speech, but wouldn't let it dominate his address. Today, they said, belonged to the graduates, more than 2,000 of whom are receiving their diplomas.
In fact, relatively few of the "Fighting Irish," as Notre Dame's sports teams and community members are known, have been among the protesters.
"Almost all of the opposition has been generated from groups outside the university," said the Rev. Richard McBrein, a Notre Dame theology professor.
Nationally, too, the Notre Dame hubbub appeared to be a debate the president is winning -- even among Catholics. One poll found 56 percent of all voters, and a whopping 60 percent of Catholic voters -- support Obama's appearance.
Even so, in addition to individual hecklers shouting interruptions during Obama's speech, some students bore silent protest.
"We are planning on putting a symbol on top of our mortarboards with a cross and a pair of baby feet," said one student, Stephen Govea, in advance of the speech.
Many did -- but others displayed symbols such as an "O" on their mortarboards in support of Obama.
A few students said they would boycott graduation.
"He may not see us on commencement day, but we are planning on praying," Andrew Chronister said. "And prayer can reach across space."
The most visible protests have been organized by outsiders like former presidential candidate Alan Keyes, who was arrested during a protest and then released, and Randall Terry, 50, the outspoken, sometimes in-your-face former head of Operation Rescue who was arrested a week ago and later sent his flock one by one into a polite police dragnet, where they were arrested for trespassing.
"Let's start filling the jails now," Terry said, "so we can have a witness that reaches to the world against this treachery and this betrayal."
Though the numbers of protesters leading up to the speech was relatively small, Terry predicted there would be hundreds more protestors during the Obama address -- and possibly hundreds more arrests.
Terry, the one-time Pentecostal lay missionary, spent much of the 1980s leading anti-abortion activists in large scale acts of civil disobedience -- including blocking entrances to family planning and medical facilities where abortions were performed. His protests garnered national media attention and frequently landed him in jail. In the years since he left Operation Rescue, he's run for public office twice -- and lost twice.
But now, he is back in the limelight, helping lead the six-week-old Notre Dame anti-abortion protest.
"Notre Dame is the premier institution of the Catholic church in the western hemisphere," Terry told ABC News. "Obama is the premier promoter of child killing in the western hemisphere. When you have that kind of epic thing going on, it demands a response from the whole Catholic world."
Terry converted to the Catholic faith a few years ago and has seized on the Obama commencement address at the famed Catholic university as a way of pushing the abortion issue back to the forefront of public consciousness.