According to Michael Azerrad's 1993 Nirvana biography Come as You Are, "Polly" is based on the true story of a female rape victim from Tacoma, Washington. The girl, 14, was abducted in 1987 while returning from a punk rock show, and was raped and tortured with razors and a blowtorch by her abductor. Cobain's only narrative flourish is that the victim manages to escape by flirting with her captor, convincing him to trust her. This allows her to escape while he stops for gas.
In the liner notes to Nirvana's 1992 compilation Incesticide, Cobain expressed disdain for an incident which occurred after the song's release on Nevermind. "Last year, a girl was raped by two wastes of sperm and eggs while they sang the lyrics to our song 'Polly,'" he wrote. "I have a hard time carrying on knowing there are plankton like that in our audience."