A small number of graduates say they won't participate in Saturday's commencement address. Others plan to wear visible signs of protest on their caps and gowns.
Sunday on the Notre Dame campus there will be pomp, circumstance and spectacle.
Anti-abortion activists are already skirmishing with police. They plan to protest the president's visit, angry that a Catholic university would have a pro-choice politician who supports embryonic stem cell research deliver the school's commencement address.
"The concern is whether the University of Notre Dame, a Catholic university, upholds Catholic teachings or not. And in this case they are betraying the Catholic faith," said Patrick Reilly, Notre Dame student.
More than 70 Catholic bishops have sharply criticized the invitation. Not one has spoken out in favor. And this year, for the first time since 1883, Notre Dame won't award its most prestigious medal. The Catholic scholar who won it turned it down in protest.
"I wasn't expecting this much flak," said Fr. Richard McBrien, Notre Dame theology professor.
Fr. Richard McBrien says universities are supposed to be a forum for the free exchange of ideas.
"The overwhelming majority of graduating seniors, faculty, and staff are delighted and honored that President Obama is coming," said Fr. Richard McBrien.
Last November, Obama won the Catholic vote outright. And this week national poll found that two out of three Catholics say Notre Dame should not rescind its invitation.
"There's always protests. I think it's an honor president is speaking. I think it's a non-issue," said Mayor Daley.
At Holy Name Cathedral many parishioners say 'he's the president, let him speak.'
"I just think people should get that worked up about it," said Bernie Coleman, Catholic.
But Nancy Madden, whose daughter is an alum, says Mr. Obama's political views are an insult to the Catholic Church.
"It's an utter disgrace," said Nancy Madden, mother of Notre Dame alum. "If I was one of those graduate's parents I would not go to the graduation. Absolutely not. My daughter and son-in-law would not even participate."
The White House says President Obama will address the controversy surrounding his visit to Notre Dame in his speech on Sunday.