The name of the mission "I Need Your Clothes, Your Boots and Your Motorcycle" is a reference to Terminator 2, in which Arnold Schwarzenegger says the same line.

The achievement "Assassin's Greed" is a reference to the Assassin's Creed series.

A Zastava M70 was supposed to appear in game, but was most likely replaced with the AK-47. It can be seen during the second trailer for the game, "Looking For That Special Someone".

The name of the mission "The Master and the Molotov" may be a reference to the novel "The Master and the Margarita" by Mikhail Bulgakov.

If Playboy X is killed, it is possible to go to his apartment and open the wardrobe to get a change of clothes that look like the outfit worn by Claude, the protagonist of Grand Theft Auto III.

The achievement/trophy "Auf Wiedersehen Petrovic" is a reference to the British comedy-drama, "Auf Wiedersehen, Pet".

The achievement "Warm Coffee" is a reference to the controversial "Hot Coffee" mod for Grand Theft Auto: San Andreas.

Many street names in Bohan are named after prisons, such as, Leavenworth Ave, Alcatraz Ave, Sing Sing Ave, Guantanamo Ave, Attica Ave, San Quentin Ave, Folsom Way, Rykers Ave, and Joliet Street.

There are references within the game's data files to a nightstick weapon, but no such weapon is available in the final game.

References to conditions relating to snow can be found in the game's files. This suggests that snow was considered as a weather condition at one point during development.

During the introductory cutscene of The Lost and Damned, while The Lost Brotherhood are riding in formation down the streets of Liberty City, Niko Bellic can be seen walking on the sidewalk in his default attire, bumping into a pedestrian and speaking in Serbian to the person. Niko's cameo appearance in Alderney is somewhat incongruous, as he would still be confined to Broker and Dukes during this mission of The Lost and Damned.

There are two scrapped haircut designs in the game: one resembling helmet-hair, and the other a buzz cut. These still exist in the game's data and can be modded in.

In the third trailer for the game, "Move Up, Ladies", the mission "The Cousin Bellics" is shown during the day while in-game the mission takes place at night.

The pool cue from the pool mini-game is categorized as a weapon, but cannot be acquired outside the context of the mini-game, and thus cannot be used as a weapon. It has all the necessary data, including a HUD icon.

An unused map icon representing a boat can be found in the game's files. Its file name is radar_boattour, suggesting that a boat tour service was once available in the game.

Internal files call the Beechwood City area of Broker "Grayfords", suggesting that Grayfords was Beechwood City's original name.

In multiplayer, if one player kills another with a vehicle, the HUD may say that they "gouranga'd" the other player. This is a reference to the original Grand Theft Auto, where if the player runs over a line of Hare Krishnas, they get a Gouranga bonus.

The setting of the game was originally going to be Liberty State, rather than just Liberty City, and it would have included countryside surrounding Liberty City, mountains based on the Adirondacks and Catskills, and possibly The Caraways.

An MP5 was originally going to be the SMG as seen in early pre-release screenshots. It had a 15 round magazine. An image of Niko holding it confirms this. Niko would presumably fire it with both hands on the pistol grip, like the Micro SMG. Its design was later replaced to resemble the S&W MP10.

The achievements/trophies "Join The Midnight Club" and "Top The Midnight Club" are possible references to the Midnight Club series which is also by Rockstar Games.