In the harbor, you'll find a dirty purple bunny doll that's been dragged up from the ocean. This is a reference to an Easter-egg in Saints Row 2.

Professor Genki has a 0.05% (1 in 2000) chance of spawning in most neighborhoods of Steelport. And a 0.25% (1 in 400) of spawning in Yearwood. Whenever he spawns, Genki has a 50% chance of being unarmed, a 35% chance of having an Annihilator and Electric Grenades and a 15% chance of having a Stun Gun and Molotov Cocktails. If the player is able to kill Genki he is rewarded with $100,000.

In one of the game's trailers (created by Tim & Eric of Adult Swim fame) it is revealed that Professor Genki was a renowned professor of science at the Science University College of Science. Genki taught along side Todd, his pet cat whom he loved. Genki, fearing his own mortality, set to work on creating a magical device that would fuse the two together so that they may live forever in harmony as a half-man half-cat being. The experiment was a success. People were in awe of Professor Genki's new form, as his head had morphed into that of a cat. He then became the international spiritual leader, replacing the Pope. The experiment wasn't without side-effects, as Genki's enlarged brain gave him powers far beyond any mortal and an insatiable appetite for wet cat food and human brains. He became all powerful, supreme and a worshiped leader. The nature of Genki was irreversible.

If Male Voice 3 is selected for The Protagonist during the mission "The Belgian Problem", when the ornament is dislodged The Protagonist will yell, "Familiar with Agincourt, you prick?". Then, when the decision presents itself, The Protagonist remarks "I'm sure there's a St. Crispin's Day joke in here somewhere...". Both are references to the 100 Years War between England and France, specifically the Battle Of Agincourt (which took place on St. Crispin's Day), where the English routed a numerically superior French army; Male Voice 3 is English, while Phillipe Loren is often implied to be French (despite his constant pleas that he is actually Belgian).

As part of a promotion for Saints Row: The Third in France and the Netherlands, THQ produced 25 replicas of the Penetrator, a four-foot purple dildo weapon from the game, to be sent out to game reviewers.

There is a Johnny Gat version of the Keyboard Cat meme hidden in one of the game's missions.

The main character of Saints Row: The Third was originally going to be an undercover cop infiltrating the Saints, and the story was more choice-driven. The idea was scrapped after the first six months of development because the developers didn't think the concept felt like a Saints Row game.

In one cut scene you are shown comic book covers. They are made by "Volition Comics", a nod to the game's developers Volition Inc.

In the Safeword crib is a PlayBoy-like magazine called BoyToy. The front cover states that the magazine contains an interview with of Johnny Gat, and features a topless picture of Shaundi that was part of Playboy's fifth edition of Playboy's "Virtual Vixens" in 2008.

There is a rabbit found in one of the game's gang operations that appears to be identical to the other easter egg rabbit of the series, but smaller and yellow.

If nitrous is in effect when you store a vehicle, the flame effect will remain in the garage when the vehicle is removed.

In Kinzie's Warehouse is an article based on Lin, a character from Saints Row, who was killed and was available to call as a homie in the form of a zombie. When Pierce sees this article during his first tour of her warehouse, he will snatch it.

During the "Zombie Attack" mission, the protagonist will also make mention to Lin being brought back as a zombie when using the Male Voice 1.

An auto-tuned voice for the protaganist was going to be used, but was cut.

The "Angelmania" taunt is a reference to "Hulkamania", made famous by professional wrestler Hulk Hogan, the voice actor for Angel De LaMuerte. Spoiler:Angel performs this move during the mission "3 Count Beat Down", after regaining his mask.