The album version of the song starts with a slowed-down voice stating "Don't worry, I won't hurt you. I only want you to have some fun." Prince shares lead vocals on the track with members of his band The Revolution, namely Dez Dickerson, Lisa Coleman and Jill Jones. Originally conceived to be a three-part harmony, it was later decided to separate out the voices that started each verse.

Some music critics have suggested Phil Collins' 1985 song "Sussudio" sounds very similar to "1999". Collins confirmed this claim, and remembers listening to "1999" frequently while he was on tour with Genesis