The song is a description of Tennant's Catholic upbringing and education at St Cuthbert's High School in Newcastle upon Tyne. The song uses extensive samples from Latin masses (specifically, Tennant reciting a part of the Confiteor, and other sounds recorded at locations such as Westminster Cathedral) and religious imagery throughout to reinforce the feel of the song. Tennant has said that he wrote the lyrics in 15 minutes, purging his emotions in a moment of frustration and anger.
At the time of the single's release, British DJ Jonathan King accused Pet Shop Boys of plagiarising the melody for "It's a Sin" from Cat Stevens' 1971 hit "Wild World". He made the claims in The Sun newspaper, for which he wrote a regular column during the 1980s. King went so far as to release his own cover version of "Wild World" as a single, using a similar musical arrangement to "It's a Sin", in an effort to demonstrate his claims. This single flopped, while Pet Shop Boys sued King, eventually winning out-of-court damages, which they donated to charity.