Guitarist Ryan Ross recalled to VH1: "That was really cool. I walked in one day and these guys were talking about the song and they said, 'Why don't you try to sing this?' I sang it because it was me and Jon's (bassist Jon Walker) song, (so) I knew the song well. We did it and everyone thought it was cool. It's still one of the coolest songs on the album.
The lyrics for "Mary, Did You Know?" were written by Christian singer and comedian Mark Lowry, after his pastor asked him to write a Christmas musical for their church. Southern gospel musician Buddy Greene later added music to his words.