- The European version has altered at least one line of dialogue in order to convert the measurements to the metric system.
- Early Footage shows scenes cut from the final version: Snake battling a Harrier Jet at the George Washington Bridge, Snake shooting soldiers with a FAMAS Assault Rifle, Snake in Arsenal Gear alone and a scene where Snake is chased by a flood throughout the Stricken Tanker.
- Originally featured a sub section where Snake was chased by a flood inside the Tanker. This idea made it into production, but the idea was later scrapped.
- The much-delayed European version of the game shipped with an additional DVD ('Metal Gear Solid 2: Sons of Liberty' - Making of the Hollywood Game (2002)) containing unreleased early trailers, production notes, and an hour-long documentary on the game's production.
- In the Japanese version, Solidus supposedly says something as he's falling from Federal Hall (it's unclear what he says, however). In other versions he's silent, although his mouth still moves as if he's talking.
- Released in November 6th, 2002, Metal Gear Solid 2: Substance, an expanded version, was released. Similar to Metal Gear Solid: Integral for the first Metal Gear Solid game, this version included VR training missions, a set of five special missions called "Snake's Tales", and the way to play as either Snake or Raiden in either part of the mission.
- The European and Japanese versions contain levels and other items not found in the US version, such as the "Casting Theater" and "Boss Survival" modes. Additionally, the European version contained a playing level that was significantly harder than all other levels (including Extreme), called "European Extreme". These are all included in Metal Gear Solid 2: Substance (2002).
- In the European and Japanese versions, it's possible to get a suppressor for Snake's USP. This was removed from the North American version but is included in at least one version of Metal Gear Solid 2: Substance (2002).
- In the North American and Japanese versions, you can find the Shaver on all difficulty levels. In the European version, you can only get it on levels Hard and higher.
- A brief scene featuring Raiden crossing the oil fence after Emma is shot was added to the Japanese and European version and included in versions of Substance.
- A brief scene after defeating Fatman is added to the Euro-Japanese version where we can hear Fatman struggling to get to a nearby crate.
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