Obama's relationship with his former pastor Rev. Jeremiah Wright also came into question, specifically Obama's understanding of Wright's full range of controversial remarks, more than a year ago, when he disinvited his longtime pastor from a campaign event.
Wednesday, Obama once again denounced Wright's sermons which included, among other things, the charge that the United States brought on the 9/11 attacks with its own "terrorism" but defended the church and his longtime pastor's 30-year career citing his work "in ministries, on HIV/AIDS, prison ministries, providing people with the kind of comfort that we expect in churches."
Clinton reiterated her criticism of the Wright relationship, saying that, based on his sermons, Wright would not have been her pastor and that she would have left his church if she had heard them.
"For Pastor Wright to have given his first sermon after 9/11 and to have blamed the United States for the attack...I would have not been able to stay in the church," Clinton said. "You can pick your pastor. You can't pick your family, but you can pick your pastor."
In an ABCNews/Washington Post poll released this week, 59 percent of adults and 72 percent of leaning Democrats approved of the way Obama handled the Wright controversy, though concerns remain among Democrats that the subject would be revisited by the Republican nominee in the general election.
Obama also faced questions about a controversial supporter of his, Bill Ayers who was once a member of the violent radical left group Weather Underground seeking to overthrow the U.S. government. The two men served together on the board of a Chicago nonprofit.
"The notion that somehow, as a consequence of me knowing someone who engaged in detestable acts 40 years ago when I was 8 years old, that somehow reflects on my values is crazy," Obama said.
Clinton framed the association in the context of the general election, "What they did was set bombs, and in some cases people died. I know Sen Obama is a good man and I respect him greatly but this is certainly something the Republicans will be raising."
Obama countered, "I don't think Sen. Clinton would make her own vetting standard. Cause President Clinton pardoned 2 members of the weather underground. Which is a bigger deal than serving on a board with someone."
Clinton had her turn in the hot seat during the debate as well, responding to her widely criticized embellishment of the details of a trip she took to Bosnia as first lady in 1996, where she described landing "in an evasive maneuver" "under sniper fire." Video footage later revealed Clinton participating in a greeting ceremony with school children on the tarmac.
Responding to a video question submitted to ABCNews by Pittsburgh resident Tom Rooney, who said Clinton lost his vote over the Bosnia flap, Clinton said "I'm embarrassed by it, I've apologized for it, and I've said it was a mistake."
Though his campaign has criticized Clinton for her erroneous retelling of the Tuzla visit, on stage, Obama gave his rival a pass on the matter.
"I think Sen. Clinton deserves the right to make some errors once in a while," Obama said. "I think what's important is to make sure that we don't get so obsessed with gaffes that we lose sight that this is a defining moment in our history."