During the mission, "Clean Getaway", while Niko and Vlad are walking to Vlad's car, Vlad is nearly hit by a Taxi and yells "I'm walking here" at the driver. This is a reference to a scene in the film "Midnight Cowboy", in which Dustin Hoffman is almost hit by a taxi and yells the same phrase. It may also be a reference to the film "Back to the Future Part II", in which Martin McFly Junior is almost hit by a car while crossing the street and yells the same phrase repeatedly.

In 2010, a lawsuit was filed by Brazilian composer Hamilton Lourenço da Silva with the Civil Court in Barueri against Rockstar Games and Synergex Brazil to restrict trading and distributing of Episodes From Liberty City in Brazil, and Worldwide, due to the song "Conga Kid", which is featured in The Ballad of Gay Tony, having sampled from his song "Bota o Dedinho pro Alto" without his permission. The injunction stated that a fine of R $5,000 (US $3,000) would be issued for each day the expansion was continued to be sold.

In The Lost and Damned, there was originally a skate park, but it was cut. You would not use a skateboard, but instead a motorcycle. There are still files hinting at its existence.

In The Ballad of Gay Tony, there was going to be a completely new vehicle introduced, the Robin, before it was scrapped. The only existence left of it is some handling files.

The third trailer for the game shows that Mikhail Faustin originally had grey hair and a different hair style.

Both Roman's clothing and hairstyle were changed during development, as seen in a pre-release screenshot.

The "Vlad Glebov" trailer for the game shows a black variant of the Taxi, which is never seen in the final version.

Niko's default outfit did not have a white stripe on the collar during development. This can be seen in multiple pre-release screenshots.

During development Ilyena Faustin wore different clothes, which can be seen in the second trailer for the game.

The second trailer for the game shows that Real Badman didn't originally wear a hat, unlike in the released version.

Originally in The Lost and Damned mission, "Politics", Johnny was supposed to get a uniform to pass by security. This also means that Johnny may have been able to have changed outfits in development.

The Fight Club was originally going to be introduced in The Lost and Damned, but it was cut until The Ballad of Gay Tony. There are still files referencing it in The Lost and Damned.

Female police officers were originally going to be implemented in the game before being cut. One can be seen in the first trailer for the game.

During development Michelle had a different face to the release version, as seen in the "Move Up, Ladies" trailer.

In the PC version of the game, the cook on the ship at the beginning of the game has a full beard; however, in the console versions of the game, he is clean shaven.

In the mission, "Wrong is Right", an email from a "Larry Ligner" sent from ligner@goldberglignerandshyster.com can be found on Oleg Minkov's computer. This would suggest that Larry was an early name for Patrick Ligner.

In The Ballad of Gay Tony, during the mission, "Boulevard Baby", a low quality map of Salem, Massachusetts can be seen on the desk in Vic's office.

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

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.