During the briefing for the second act of the game, Sunny can be seen walking around playing Penguin Adventure, the first game Hideo Kojima ever worked on, on a PlayStation Portable. If the player gets close enough with the Metal Gear Mk. II, music from the game can be heard playing.

One of Hideo Kojima's early ideas for the game's ending was to have Snake and Otacon turn themselves in to the United Nations for breaking the law (presumably for the crimes they committed while operating as Philantropy during Metal Gear Solid 2: Sons of Liberty), and be convicted and executed. The rest of the developers reacted negatively to this ending, which resulted in Kojima changing it. However, it's possible a remnant of this ending was left behind in the form of the game's end credits theme, a cover of "Here's to You", originally written for the 1971 Italian docudrama film "Sacco & Vanzetti". Both the song and film are based on the real-life case of two Italian anarchists who migrated to the United States in 1908, and in 1920 were convicted and sentenced to death after being accused of murdering two people during an armed robbery. The original 1971 recording of the song would later be used as the opening theme to Metal Gear Solid V: Ground Zeroes.

In the Japanese release of the game, there is hidden meaning in the game's ending. Spoiler:Big Boss is portrayed by voice actor Chikao Ōtsuka; father of Spoiler:Solid Snake's voice actor Akio Ōtsuka.

Hideo Kojima has claimed that the two had fallen out years before and had not spoken to one another since, and Kojima intentionally cast Chikao in the game hoping to help patch things up between the two.

After defeating a BB member in their Beast stage, they will shed their armor and go into their Beauty stage of the fight. If the player avoids them for about two to three minutes while they are in this stage, both the player and the BB member chasing them will be transported to a white room.
If the player uses the camera in this white room, the BB member will pose randomly. Even more, if the player uses the iPod and plays the song "Oishii Two-han Seikatsu", the BB member will briefly dance to the song.

During the final showdown Spoiler:between Snake and Ocelot, the characters' life bars change names and graphics to represent the life bars featured in the other main Metal Gear Solid games. First it's Solid Snake and Liquid for Metal Gear Solid, Solid Snake and Liquid Ocelot for Metal Gear Solid 2: Sons of Liberty, and finally Naked Snake and Ocelot for Metal Gear Solid 3: Snake Eater.

With each change, the background music also changes to the representative theme from each title.

During the "commercials" at the start of the game, series creator Hideo Kojima can be seen observing at the sidelines of the "Bomb Shelter Buffet" commercial.

During Act 3, it's possible to see a "man" stalking Snake as he follows the Resistance Member. Occasionally when turning around, the cloaked figure will hide behind a corner. Spoiler:It is believed that this is the 3 Dwarf Gekkos that attack Snake and the Resistance later in the chapter.

Rosemary wears different sweaters depending on the day of the week.

Although Metal Gear: Ghost Babel is non-canon, it is mentioned in the game's weapons description for the Five-seveN, saying that Solid Snake used the pistol in Galuade.

During the final battle against Spoiler:Liquid Ocelot, if you leave your controller idle when Snake is grabbed by the neck, the boss will kiss Snake on the cheek and regain stamina. By letting this happen, you'll earn the achievement "You're pretty good".

The game currently holds the Guinness World Record for 'Longest Cutscene in a Video Game', clocking in at 71 minutes for a single cutscene.

In an interview for a Japanese magazine, Hideo Kojima claimed that a 50GB Blu-ray was not sufficient for the game. Apparently, the team had to compress certain parts of the game to get it to fit on the format, and foreign voice tracks were cut completely.

The AI of the Patriots are named GW, AL, TR, and TJ, after George Washington, Abraham Lincoln, Theodore Roosevelt, and Thomas Jefferson. They are compared by Eva as a "sort of digital Mount Rushmore". The AI core that unites them is JD (John Doe).

There is a representation of Mount Rushmore on Outer Heaven with the faces of Big Boss and his Sons.

Hideo Kojima originally wanted the Beauty and the Beast Corps to be completely naked in the cut scenes. The motion capture actors were even asked to preform the motion capture nude, though this could also not be used in the game. The Beauty and the Beast Corps were, instead, given cat-suits, which could still show off their bodies without affecting the rating.

In the second chapter before the fight against Laughing Octopus, all the canonical titles of the series are presented in small cases (like the PS3's selection system). There are also 2 cases which read "Under construction".

This is a reference to "Metal Gear Solid: Peace Walker" and "Metal Gear Rising: Revengeance (then known as Metal Gear Solid: Rising)" which were still in development at the time.

Johnny's grandfather, the Johnny from Metal Gear Solid 3: Snake Eater, was supposed to make a cameo appearance Spoiler:during Johnny and Meryl's wedding at the end of the game. Grandpa Johnny's cameo was cut from the game, but official artwork of him appears in the illustration book Metal Gear Solid 4: Master Art Works.

In an April Fool's Day trailer, Altaïr from Assassin's Creed was shown fighting Metal Gears. At the end of the trailer, he removes his robe to reveal Solid Snake. Though seen as a joke at the time, Altaïr's robe can still be unlocked in game.

The battle with Screaming Mantis is a reference to the original battle with Psycho Mantis. The boss music is "Mantis' Hymn." When Mantis screams 'BLACKOUT!', the screen will turn black and a green "Hideo 2" will appear in the corner. If you try to switch the controller port to Player 2, you can't move and Otacon will tell you that the trick won't work this time. Spoiler:After the battle, Psycho Mantis' ghost will appear and try to read your memory card again. He will also try to move your controller via the rumble feature.

In Metal Gear Solid 4, the all-female haven troops cannot be knocked unconscious by grabbing their crotch after a body search (as it turns into a grope). If Snake tries this, the soldier will start yelling "Pervert!", "You idiot!", "If you don't cut that out...", or "You men are all the same!" They will soon retaliate with an incapacitating kick. That said, there's a slight chance they will say, "Hey, you're pretty good at that."