"Holy Wars…The Punishment Due" is the opening track of thrash metal band Megadeth's 1990 album Rust in Peace. The song has an unusual structure, shifting at 2:26 after an acoustic bridge by Marty Friedman to a different, slower and heavier section called "The Punishment Due", before speeding up again. The entire song is commonly referred to as "Holy Wars".

The lyrics deal with the Northern Ireland conflict. In an interview with the UK magazine Guitarist, Mustaine says that he was inspired to write the song in Northern Ireland, when he discovered bootlegged Megadeth T-shirts were on sale and was dissuaded from taking action to have them removed on the basis that they were part of fund raising activities for "The Cause" (i.e. the Provisional Irish Republican Army). "The Punishment Due" is based on the popular Marvel comic book character, the Punisher.

A cover version of the song is playable in the band simulation game Rock Revolution. The master recording is purchasable as part of the Rust in Peace album pack on the Rock Band band simulation platform, is playable in the Guitar Hero: Warriors of Rock game, and is available as DLC for Rocksmith 2014. The "Holy Wars…The Punishment Due" video was filmed in August 1990 (around the time of the Gulf War in 1990). It depicts news footage of various armed conflicts, mainly from the Middle East interspliced with footage of the band playing.

7" edition

12" edition

CD edition

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