But that wasn't it. And when pressed, he drew another blank.
"Seriously?" asked moderator John Harwood, one of the CNBC debate hosts. "You can't name the third one?"
"The third agency of government I would do away with — the Education, the Commerce. And let's see. I can't. The third one, I can't," Perry said. "Oops."
Later in the debate, Perry revisited the question and said he meant to call for the elimination of the Energy Department.
On Thursday, Perry said he just couldn't think of it.
"There were so many federal agencies that come to mind, that I want to get rid of, that the Energy Department would not come out," he said in an interview taped for ABC's "Good Morning America."
He's trying to turn it to his advantage. On NBC's "Today" show, Perry sought to make the best of the gaffe, saying that forgetting the name of one of the agencies illustrated the "core point" of his campaign — that there are too many agencies. He's already blasted an email to supporters asking them, "What part of the Federal Government would you like to forget about the most?" His website now asks them to vote for one.
The immediate fallout has been brutal.
"We all felt very bad for him," Michele Bachmann, the Minnesota congresswoman also running for the nomination, said after the debate.
"Rick Perry just lost the debate. And the entire election. You only had to name three," Tim Albrecht, the top spokesman for Iowa Gov. Terry Branstad, who is unaligned in the GOP race, tweeted from his personal account.
"Perry response will be on highlight reels for years to come," tweeted businessman Jack Welch.
His campaign obviously recognized just how bad it was. In dramatic fashion, Perry bee-lined it to the "spin room," the place where reporters gather to interview campaign surrogates, and immediately indicated that he knew he had made a really bad mistake. The first words out of his mouth as reporters crowded around were: "I'm glad I had my boots on because I really stepped in it tonight."
The next few days will shed light on whether voters care about the misstep — and punish him for it.
Over the past two weeks, Perry has sought to prove he's still a credible challenger to Romney by rolling out detailed policy proposals. But he's found himself dogged by suggestions that he had been drinking or taking drugs when he gave an animated speech in New Hampshire. It went viral online, prompting Perry to state that he was not, in fact, under the influence of a substance.
NBC's "Saturday Night Live" did a widely viewed Perry parody last weekend.
In recent days, the candidate started to take his message directly to voters by running sunny, biographical television ads in early primary states like Iowa and New Hampshire. It's an effort to reintroduce himself to Republican primary voters in a safer setting that circumvents the news media.
Wednesday's was the latest tough debate for the GOP candidate who has struggled in the national spotlight since entering the race in August, the last time he was at the top of polls. His standing has fallen throughout the fall, and he's fighting to gain ground less than two months before the leadoff Iowa caucuses.
He has committed to four more debates in a year when the GOP electorate is clearly tuned into them, but his advisers are considering skipping future ones.
Presidential debates have offered pivotal moments for decades, from Al Gore's audible sighs in 2000 to Michael Dukakis' tepid answer about the death penalty in 1988.
A statement by Gerald Ford in a 1976 presidential debate is among the most memorable, however. Ford famously baffled audiences when he said, "There is no Soviet domination of Eastern Europe" and refused to back down when pressed by the moderator. The moment haunted the rest of his losing campaign.
Perry canceled private fundraisers in Tennessee and instead headed to New York for another round of interviews, including the appearance with Letterman. His next public campaign stops were scheduled in South Carolina on Friday — the day before yet another debate.
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