There is a family of three monkeys and a teddy bear hidden in the first playable level of the game.

On the level "Crow's Nest", you can find a solder knocking on a door wanting ammo, while the man behind the door will ask for a password to get in. Depending on what difficulty you are playing, the conversation is different. These conversations are performed by the online comedy group, Rooster Teeth, famous for their Halo series, Red vs. Blue.

In the multiplayer map "Sand Trap," it is possible to flip an Elephant over. When A Spartan/Elite tries to flip it back over, it will say "Hold RB to flip... wait, what? How did you do that?"

In Halo 2, Halo 3, and Halo: Reach, the bomb in the Assault multiplayer game mode sometimes has a hidden message written on it. The possible messages include "Thus I Refute Thee", "Kiss It Goodbye", "Hold Onto Yer Butts", and a hieroglyph of a Spartan helmet along with the two-fingered peace sign and "xoxo & hearts".

The first message, "Thus I Refute Thee", is a reference to the logical fallacy of appealing to the stone originating from the English writer Samuel Johnson, who during an argument about how it was impossible to refute idealism, kicked a large stone and said the quote. This quote was put on the bombs in Halo 2 by Bungie senior employees Robert and Lorraine McLee, in response to a conversation about Marathon and philosophy between two members of the Halo fan website Team 7HR33, who agreed that it would be "the uber-quip" to inscribe on the side of a gun.

In the level "The Covenant" on Normal or higher difficulty, the Windows voice program "Microsoft Sam" can be found commenting on the game and it's developers on the right ledge of the Citadel, whilst on the left ledge can be heard the song "Siege of Madrigal" from Bungie's previous game Myth: The Fallen Lords.

Although Spartans and Elites have different body shapes, they use the same hitbox. Because of this, there's a glitch where bullets, grenades, and Needler rounds will pass unimpeded through part of an Elite player's neck without dealing damage to the player.

During the game's open beta test, a medal was discovered called "Cheneymania!" that could be earned by killing ten players consecutively with a shotgun and without dying. This was a reference to the then-current vice president of the United States, Dick Cheney, who one year prior in 2006 had accidentally shot attorney Harry Whittington while they were out quail hunting. After players and other Bungie developers noticed, they changed the name of the medal to "Shotgun Mania", and then to its final name "Open Season". According to multiplayer announcer Jeff Steitzer, it was originally planned for him to shout "Cheneymania!" as a hidden voice line that would have been triggered under very rare circumstances if the player were to kill their own teammates. This line was cut from the game before the open beta test began, but the Cheneymania! text was left in as an oversight.

In the game's last level, Spoiler:shortly before reaching the Frigate, there is a Grunt hidden at the end of a small pathway around some rocks. The Grunt will taunt Master Chief, and then proceed to plead for his life. However, if Thel Vadam sees the Grunt, he will kill him before the Grunt has a chance to finish talking.

Pressing down on both thumbsticks while at the loading screen on December 25th will display a wider view of the Halo ring. Looking closely, it's possible to see the words "Happy Birthday, Lauren!" spelled out on the ring's surface.

In Halo 2, if you start the campaign level Gravemind on Legendary, an Easter egg can be spotted during the opening cutscene. After the Gravemind finishes his long conversation with Thel Vadam and Master Chief John-117, the camera fades to the High Charity station. Inside there are Brutes defending the room where the Prophets are hiding from the Elites. When the Grunt climbs the arch and the camera focuses to the crowd up ahead, you can see standing in the crowd of Grunts a hidden 2D image of a man in nothing but gym shorts looking at the floor, with his hands behind his head. Dubbed the "Half-Naked Guy", this man is Bungie co-founder Jason Jones.

In Halo 3, the Half-Naked Guy can be found again standing on a small nook in an out-of-the-way hidden area at the beginning of the last campaign level, specifically in a dark room with a lethal chasm next to the hallway for the seventh Terminal.

UK chat show host Jonathan Ross voices one of the marines that helps Master Chief in the campaign, although it is an extremely rare occurrence for one of his lines to come up.

In the beta release's multiplayer mode, if you can angle the camera correctly while on a vehicle, it will clip through your Spartan's helmet and reveal a face underneath. This is a photo of Marcus Lehto, Bungie's creative director from 1997 to 2012.

According to 3D artist Eric Arroyo, he built a Xenomorph Warrior from the Alien series inside Halo 3's engine as part of early experiments for a potential Aliens style encounter. The idea never advanced beyond prototyping, and plans for a crossover with the Alien franchise were scrapped with it.