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.

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.

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.

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.

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

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.

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

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

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

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

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.

It was originally intended for the game to include flyable planes and jets, however according to a Q&A session by Rockstar Games, they were cut because the map was too small.

An entry for a flamethrower exists in the game's WeaponInfo.xml file, but only the title "FTHROWER" remains, with no extra data to make it playable.

If a pirated copy of the game is recognized, the in-game camera will swing wildly around during play.

An early pre-release screenshot of Playboy X depicted him wearing a different colored sweater.

On the in-game website Yourmexicandoctor.com, two fictional drugs named Hingmyralgan and H4PP1 are listed. These drugs were first found in Manhunt 2, also by Rockstar Games.

In The Lost and Damned, in the mission "Heavy Toll", Johnny refers to the Assault Shotgun as "an American firearm". He is only partially correct, because the Street Sweeper is a copy of the South African Armsel Striker, produced under license in America by the Cobray Company.

In The Lost and Damned, when calling Jim for an Automatic 9mm, Johnny will call it a 'semi-automatic 9mm' instead.