In the mid-1980s, Summer was embroiled in controversy after she allegedly made anti-gay remarks regarding the then-relatively new disease, AIDS, which as a result had a significantly negative impact on her career. Summer, by this time a born-again Christian, was alleged to have said that AIDS was a punishment from God for the immoral lifestyles of homosexuals. Because of this alleged quote, thousands of her records were returned to her record company. Years later, Summer publicly denied that she had ever made any such comment, and in a letter to the AIDS campaign group ACT UP in 1989 said it was "a terrible misunderstanding. I was unknowingly protected by those around me from the bad press and hate letters... If I have caused you pain, forgive me." She apologized for the delay in not making a response earlier and closed her letter with Bible quotes (from Chapter 13 of 1 Corinthians).
Also in 1989, Summer told The Advocate magazine that "a couple of the people I write with are gay, and they have been ever since I met them. What people want to do with their bodies is their personal preference." A couple of years later, she filed a lawsuit against New York magazine when it reprinted the rumors as fact just as she was about to release her album Mistaken Identity in 1991. According to a Biography television program dedicated to Summer in which she participated in 1995, the lawsuit was settled out of court, though neither side was able to divulge any details.