The group, known as the American Issues Project, brags it has run ads 7,307 times in 14 markets, calling into question the longstanding relationship between Obama and William Ayers.
"American Issues Project clearly has struck a nerve inside the Obama campaign, but even more important is the reaction of the American people, who are starting to question why Senator Obama would have such a close relationship with an unrepentant domestic terrorist," said Ed Martin, American Issues Project president, on the group's Web site.
On the Democratic side, the powerful Service Employees International Union (SEIU) is running a television ad in the battleground states of Pennsylvania, Ohio, New Mexico, Michigan, Wisconsin and Iowa that links McCain to the nation's struggling economy.
An announcer says in the SEIU ad, "John McCain said 'I know a lot less about economics. I still need to be educated.' No wonder he said we're better off than we were eight years ago. It's time for change."
While Americans routinely tell pollsters they don't like negative attack ads, presidential candidates continue to use them for one reason: they work.
"An effective negative ad can be powerful in changing the public's perception about a candidate," said John Geer, political science professor at Vanderbilt University and author of "In Defense of Negativity," a book about campaign attack ads.
Geer argues the content of negative ads are often more informative to voters about the candidates' records than positive ads with vague assertions touting a candidates' character or leadership skills.
One of the most memorable ads in presidential politics was Lyndon Johnson's 1964 "Daisy Ad" depicting a little girl picking daisies in a field before a nuclear blast to warn against Republican Barry Goldwater's foreign policy positions during the Vietnam war.
Goldwater lost by a landslide. Equally effective was former President George H. W. Bush's "Willie Horton" attack ad painting Michael Dukakis as weak on violent crime.
Geer says negative ads have only intensified in the digital age, allowing campaigns to create an ad and not have to actually purchase expensive television air time for it to get into the public debate.
"The news media give coverage to these more negative campaign ads because they're the ones that get attention," Geer said.
But Geer said negative ads could also backfire.
"The McCain ad suggesting Obama wants to give sex education to kindergartners is pushing the envelope," Geer said, "and it's being shown to be not true."
McCain's negative ads coincide with a more streamlined campaign strategy ushered in by McCain's chief strategist Steve Schmidt, known as "The Bullet" for his shaved head, who is a Rove protege.
Attack ads could also have the unintended side effect of turning off an already cynical American electorate to the presidential campaign.
Geer said the 2008 presidential election campaign has gotten particularly nasty early on.
"I am struck by how much both sides are putting up negative ads this early in the campaign," Geer said.
ABC News' Jake Tapper contributed to this report.