During development of the game, Hideo Kojima wanted the Beauty and the Beast Unit to be naked, though this would have severely affected the game's censorship rating. Yoji Shinkawa stated that the motion capture actors were asked to do the motion capture nude, though this could also not be used in the game.
During a press conference promoting the European release of Metal Gear Solid 3: Snake Eater (2004), Hideo Kojima said he would not direct this game. Shuyo Murata was set to direct instead. However, after receiving intense fan feedback (some in the form of death threats) and requests from his staff to return, Kojima changed his mind and decided to co-direct the game with Murata. He later said that this will be the last Metal Gear game he directs.
During the game you hear audio clips playing intended to be flashbacks of previous games. These are especially predominant in Shadow Moses, where the first Metal Gear Solid took place. However, the audio clips are not from the original "Metal Gear Solid" on the Playstation and PC but the re-recorded dialog from the remake "Metal Gear Solid: The Twin Snakes" on the GameCube. This is especially noticeable since in some of the audio clips Naomi doesn't speak with an accent and the dialog was slightly altered from the original.
This is the first Metal Gear Solid (1998) video game series ever where at one point of the scene you can control the Metal Gear and fight the enemies and a boss at that specific scene. All the previous Metal Gear games only involves fighting against the Metal Gears of their respective series.
Unlike regular PMC troops, the all-female Haven troops cannot be knocked unconscious by grabbing their crotch after a body search (it turns into a grope). If Snake attempts this, the soldier will yell "Pervert!" "You idiot!" or "You men are all the same!" and retaliate with an incapacitating kick. However, if wearing the Young Snake FaceCamo, they seem to enjoy the action.
According to the Metal Gear Solid 4 Database, Little Gray resembles an alien captured by the FBI. A reference appears during Act 2. In the cut-scene just after Drebin's Stryker crashes, when Naomi and Snake walk out of the Stryker holding Little Gray, the player can press X to see an image of two men and the "alien" in question. In actuality, the photo shown is a famous picture of two men with a monkey, which resulted in a conspiracy theory believing that the monkey was actually an alien. Drebin also has this picture inside his Stryker. Also, Little Gray's name derives from a euphemism for an extraterrestrial.
The first Metal Gear Solid game to feature original live action footage (mainly for the TV spots and shows during the prologue). While the previous Metal Gear Solid games only had archive live action footage for certain scenes.
This is the only Metal Gear Solid (1998) video game series where the reoccurring characters Naomi Hunter and Mei-Ling appear in their physical appearances during cut-scenes. Naomi Hunter and Mei-Ling were only characters that were contacted through the Codec receivers and never made a psychical appearances from the previous series. Roy Campbell, however, made a very brief physical appearance in the original MGS on Playstation. The Video that plays after sitting on the title screen too long sweeps the sub where Snake is deployed from and shows Roy standing in front of a map.
Four real life models were chosen for the Beauty & the Beast Unit's inner Beauty selves. They were Lyndall Jarvis (Laughing Octopus), Scarlett Chorvat (Screaming Mantis), Mieko Rye (Crying Wolf), and Yumi Kikuchi (Raging Raven).
An early version of the OctoCamo was used by Snake during Metal Gear Solid Mobile. The early version could not replicate patterns by touch, however; the player had to take pictures of colors themselves using their phone and then transfer them onto Snake's suit.
While never actually named in-game, the city in Eastern Europe is based on Prague. The bridge that appears briefly during the bike chase is a recreation of the Charles Bridge, Prague's most famous sight. The bridge crosses the Vltava river, though it referred to as the "Volta" in-game. In railway station which look like "Hlavni nadrazi" (Central Station) are Czech signs:"Tento prostor je hlidan prumyslovou televizi" - This area is monitoring by industrial camera.
Several paintings adorned the interior of the Paradise Lost Army's church hideout, portraying the events of Operation Snake Eater, the San Hieronymo Takeover, the Shadow Moses Incident, and the Big Shell Incident.
The weapons mounting of a Gekko is similar, but not identical to, the M151 Remote Weapon Station used by real-life armored vehicles. It is unclear how a Gekko's heavy weapons are restocked, since it has no obvious capacity for reloading its own weapons in the field; presumably they must withdraw once the fixed armament is depleted, though in the context of the game they have infinite ammunition. Though they are capable of carrying Dwarf Gekkos on the sides of their heads, as seen in the game's cut-scenes, this configuration is never encountered during actual game-play.
The main members of the Beauty and the Beast Corps are based on the members of FOXHOUND from the original game. Laughing Octopus is based on Decoy Octopus, and both mimic other people. Raging Raven is based on Vulcan Raven, and both are the heavy-weapons experts. Crying Wolf is based on Sniper Wolf, and both are the snipers of the groups. And lastly Screaming Mantis is based on Psycho Mantis, and both are the psychics of the groups.
This is the first game in the MGS series where the main protagonist is not captured and tortured at any point. (Though during the 3rd act in Europe Liquid corners Snake and roughs him up, he never took Snake into custody.)
This installment is the first game where the part of Liquid is not voiced by actor Cam Clarke. Clarke portrayed Liquid Snake in the original MGS under the name James Flinders, then again in MGS 2: Sons of Liberty and finally in MGS Twin Snakes. (His voice can however be heard in this game, if Snake kills too many people and his psyche gage drops too low.)
Even though the body that Paradise Lost Army had in possession was referred to as Big Boss's body, it was actually the body of Solidus Sanke from Metal Gear Solid 2: Sons of Liberty. Note that the left eye is missing like Solidus. While Big Boss is missing a right eye.