The achievement/trophy "Finish Him" is a reference to the Mortal Kombat series, in which the announcer says the same phrase at the end of the final match.

During one of the powerboat outings with Brucie Kibbutz, he will call the Statue of Happiness the "Statue of Freedom", while the subtitles still say "Statue of Happiness." This suggests that the statue might have had a different name during development, but the audio file did not get changed to reflect the statue's final name.

There are signs that the Well Stacked Pizza Co. from Grand Theft Auto: Vice City and Grand Theft Auto: San Andreas was originally meant to reappear in the game:

• Outside the store "Pizza This", the employees are still seen sporting the logo and some with "Well Stacked Pizza Co." on the back of their shirts.
• Logos and names of Well Stacked Pizza can be found at a shuttered storefront at the Alderney Casino in Westdyke, Alderney.
• The chain is mentioned on the Pißwasser website as a business partner of the beer company.
• When blocking the route of certain taxis, the driver will sometimes shout lines such as "Hurry up, I need to get to Well Stacked!" and on occasion "My Pizza Stack's gettin cold, move it!"
• Pedestrian-to-pedestrian dialog will occasionally involve whether Pizza Stack or Burger Shot is better.

The multiplayer mode "Bomb Da Base II" pays homage to the GTA III mission "Bomb Da Base Act II". In both, the player must collect explosives and place them on a ship.

Cash registers throughout the game have a button that reads "Ask CJ". This is visible through the use of a sniper rifle, zooming in on the keypad of the cash register. This is a reference to CJ from Grand Theft Auto: San Andreas.

In the Ballad of Gay Tony trailer titled "Meet Luis Lopez", Luis is seen wearing the brown and black Perseus suit, but with blue jeans. This implies that it may have been one of Luis' already available outfits.

In the Ballad of Gay Tony mission "Not So Fast", the Jewish mobster who attempts to shoot Luis in the cutscene has a Pump Shotgun, but after the cutscene, the shotgun lying on the ground is the Combat Shotgun.

There is an unused pinball animation in the game's files, meaning that pinball was likely planned to be playable at one point.

The Wooden Baseball Bat was originally going to be included in The Lost and Damned, but was cut.

In earlier versions of GTA IV, one of the Most Wanted criminals, Maxwell Caughlin, is listed on the database as Maxwell Caddy.

There are sound effects for a handheld minigun in the game's files.

Graphics for a scrapped game mode called "Zombie Revolution" can be found in the game's files.

There was originally a restaurant named "Fanny Crabs" which would be based off of the real life restaurant, "Fatty Crabs". Sound files still exist for the workers. The name is also British slang for pubic lice on a woman's genitals.

Originally, ice cream could be bought from street vendors. Sound files still exist in the game's data.

According to an interview with Dan Houser by the Official Playstation Magazine UK, Staten Island was not included in the game because the development team decided that it wouldn't be a fun location to play in.

The pistol's chamber was originally black instead of grey.

Mickey originally didn't wear glasses and wore a different outfit.

Originally, Little Jacob did not wear glasses.

The game was at one point going to have bus drivers. They were cut for unknown reasons, but they appear to be fully modelled.

There are multiple sound files for a golf kart in the original game, meaning they could have been planned to be implemented before the Ballad of Gay Tony.