The follow-up to The Best of 1980–1990 (1998), it was issued as both a single-disc CD compilation and as a multi-disc compilation called The Best of 1990–2000 & B-Sides, which included a second disc of 14 B-sides released between 1990 and 2000 and a bonus DVD.

The Best of 1990–2000 contained two newly recorded tracks: "Electrical Storm" and "The Hands That Built America"; the former was released as a single, while the latter was released on the soundtrack to Gangs of New York.

The compilation also includes "new mixes" of several songs, as well the tracks "Hold Me, Thrill Me, Kiss Me, Kill Me" (a non-album single from 1995) and "Miss Sarajevo" (which was originally credited to Passengers and also released as a single in 1995).

"Gone", "Discothèque", "Staring at the Sun", and "Numb" were remixed by Mike Hedges for the compilation.

"Mysterious Ways" is identical to the album version with the exception of a single lyric.

"The History Mix" is a video montage anthologizing the band's nineties albums and tours.