Prejean has been the topic of controversy in the media for her outspoken belief that marriage should be between a man and a woman. During the final round of the pageant, when the top five contestants are asked a question from a judge, Perez Hilton (a.k.a. Mario Armando Lavandeira), a homosexual activist blogger, asked Miss California if every state should legalize same-sex marriage. Prejean chose to stand up for her beliefs by responding, "I think that in my country, in my family, I think that I believe that a marriage should be between a man and a woman. No offense to anybody out there, but that's how I was raised."

After the pageant, Hilton openly bashed Prejean for her answer through a video blog, which he used to call her a "dumb b****." Hilton, along with the pageant owner, Donald Trump, and others believe that Prejean's answer ultimately cost her the Miss USA title, leaving her first runner-up.

Prejean said, "I knew at that moment after I answered the question ... I was not going to win because of my answer, because I had spoken from my heart, from my beliefs and for my God.... I wouldn't have answered it differently.... With that question specifically, it's not about being politically correct. For me it was being biblically correct."

Mathew D. Staver, Founder of Liberty Counsel and Dean of Liberty University School of Law, commented: "When a beautiful and talented contestant like Carrie Prejean loses the title of Miss USA because she believes in traditional marriage like the rest of us, we ought to wake up to the chilling reality of the intolerant and radical homosexual agenda. The homosexual agenda is intent on silencing America and will use the force of law to club dissenters into submission."