According to the Kurt Cobain biography written by Christopher Sanders, “Beautiful Son” was inspired by the fact that Cobain used to crossdress as a child. More generally, introducing the song during a live show in London, Courtney Love said:

This song is about boys that have problems with their mothers and are not really good… but have feminine looks. It’s about androgynous men, which you have a whole goddamn nation of.

The single’s cover artwork was designed by Love: it features a picture of seven-year-old Cobain, decorated with a frame of gift bows.