"My high school picture was cute," Clinton joked with reporters during a campaign stop Monday, the same day Spencer's alleged comments were reported in the New York Daily News.
Spencer, in an interview with The Associated Press, denied making the comments to a reporter-columnist during a flight Friday from New York City to Rochester for the first of two weekend debates between the Senate contenders.
"It's a fabrication. I would never call Hillary Clinton ugly," the former mayor of Yonkers told the AP. "That's outrageous. I didn't do it."
Clinton said comments about her appearance strayed from the issues of the campaign.
"It's unfortunate that when you don't have anything positive to say about the issues that we can get off in some pretty swampy territory," Clinton said during the stop at a senior citizens' center in Watervliet just north of Albany.
Spencer did acknowledge talking to Daily News reporter Ben Smith on the flight.
Smith told the AP that Spencer made the comments during a flight in which Spencer, his wife and Smith sat together.
The Daily News' Monday front page headline on the story screamed "GETTING UGLY," and featured the high school picture that Clinton said she liked.
"You ever see a picture of her back then? Whew," the Daily News quoted Spencer as saying. "I don't know why Bill married her."
Noting she looks different now, he chalked it up to "millions of dollars" of "work," according to the tabloid.
"She looks good now," he is quoted as saying.
Clinton adviser Howard Wolfson said Clinton has had no plastic surgery or similar appearance-enhancing work done.
"Sadly, this is just the latest in a long line of insulting and offensive comments that John Spencer has made throughout his career, and it's unfortunate that he has chosen to run a campaign based on personal attacks," the Clinton aide told the AP.
Polls have shown Clinton far ahead of Spencer in the Senate race. The Clintons recently celebrated their 31st wedding anniversary. She turns 59 on Thursday.