The Region 1 DVD release of Season 3 modifies the opening credits of the first three episodes of the season to say "Star Trek: Enterprise" instead of "Enterprise", in order to be consistent with the rest of the season.
North American syndicated version of the first episode "Broken Bow" replaces the instrumental version of "Faith of the Heart" with the instrumental "Archer's Theme" heard on most other episodes.
The music tracks from the following scenes were scored differently from internet clips released a few days before the premiere and the final version:
the Opening Scene in the cornfield
the Sickbay Assault
The premiere episode, Broken Bow, originally aired as a two-hour TV movie. As has been the case with past Trek two-hour specials, minor edits were made when the episode is syndicated as a two-parter.
The Canadian cable network Space Channel uses a different version of the closing credits. While the regular closing consists of white text on a black background, the Space broadcasts fills the top half of the screen with a picture of Earth with the Enterprise logo superimposed over it, with the credits condensed onto the lower half of the screen.
There are two versions of episode "Shockwave Part 2". It originally aired on 18-Sep-2002, but when it re-aired in its first rerun on 23-Oct-2002, it was an 'extended version', with about 1-minute 4-seconds of added footage.
The Season 1 DVD release in May 2005 included several minutes of deleted scenes for several episodes. Most of these were obvious trims for time or pacing, but a couple of more substantial cuts are also included, such as a scene from "Two Days Two Nights" showing how Archer arranged for his crew to take shore leave on Risa (including a line of dialogue from T'Pol that foreshadows the following season's episode "The Seventh").
Two versions of the third season episode, "Harbinger" were broadcast. As originally filmed, a love scene between T'Pol and Trip included a brief view of the top of T'Pol's buttocks. When UPN aired the episode in February 2004, however, the shot was censored. Canadian broadcasts of the episode, however, were uncensored. The DVD version of this scene is uncut.
Region 1 DVD release of the second season omits the tribute to the crew of the Space Shuttle Columbia originally aired at the start of the episode "Stigma".