Hideo Kojima wanted to use Kurt Russell as the voice of Naked Snake instead of David Hayter, who had previously played the role of Snake in Metal Gear Solid 1 and 2. After Kurt Russel turned the role down, David Hayter was given the part only after re-auditioning for the role.

"I had to re-audition for Metal Gear 3 to play Naked Snake...I heard that Kojima asked one of the producers on Metal Gear 3 to ask Kurt Russell if he would take over for that game. He didn't want to do it." - David Hayter

In the HD rerelease of the game, during the opening cutscene before Snake performs the HALO jump, his mask reads:
"US ARMY
METAL GEAR SOLID
snake eater"

If the player spends a long time in Spoiler:the cave after the fight with Ocelot, the screen will gradually become lighter, simulating the effect of Snake's eyes adjusting to the dark.

In the scene where Snake talks with Granin, a slow guitar-only version of Metal Gear Solid 2: Sons of Liberty's main theme will play. There's also figurines of Metal Gear Ray and Rex in the room.

It is possible to blow up food stores using TNT. Blowing up food stores will make all the soldiers in the area complain about being hungry with audible stomach growls, causing them to eat anything Snake throws at them, including poison.

A statue of Jehuty can be found in Granin's office. Jehuty is the Orbital Frame piloted by the main characters of both Zone of the Enders and Zone of the Enders: The 2nd Runner, which were also created by Kojima Studios.

In Metal Gear Solid 3: Snake Eater, the Tsuchinoko is an invisible snake that is undetectable by Radar and Thermal Goggles. Capturing and keeping it until the end of the game unlocks a special face camo that gives the player unlimited ammo on their next play-through.

The Tsuchinoko (ツチノコ) is a legendary snake-like cryptid from Japan. The name tsuchinoko is prevalent in Western Japan, including Kansai and Shikoku; the creature is known as bachi hebi in Northeastern Japan.

Early in the game, the scene where The Boss and Naked Snake are seen reaching out to each other from the Hind chopper and on the ground respectively was originally going to be different. According to Hideo Kojima in the MGS3 commentary, this scene was originally going to have The Boss release her bandana to the wind for Snake to catch, which he'd then use as a sling. However, the scene was changed because one of the motion capture actors requested that they change when Snake acquired the bandana to when The Boss throws him down into the river prior to this scene.

If EVA's HP reaches more than half and she doesn't have any serious non-story related injuries by the time they reach Zaozyorje East, checking EVA in the model viewer will have her wearing her black bikini instead of her biker outfit.

Director Hideo Kojima revealed in a Metal Gear Solid 3 commentary that The Boss was designed based on actress Charlotte Rampling.

If the player doesn't remove the transmitter from Snake after his torture session in Groznyj Grad, the path to the waterfall will be guarded by an Ocelot Unit. Later on, past the waterfall, an additional cutscene will be triggered, in which EVA removes the transmitter herself.

Because of the nature of his boss fight, The End is the only boss in the game that has no boss battle theme.

According to a commentary by Kojima, the boss battle with The Boss originally had her wearing shooting goggles to hide her tears. In addition, she was also originally to have worn a blue sneaking suit, similar to that of Solid Snake in Metal Gear Solid, so as to make her more visible. These concepts were both cut in the end.

According to Hideo Kojima, during the filming of The Boss' fight with Naked Snake at Dremuchij North during Operation Snake Eater, Eriko Hirata, The Boss' motion capture actress, started breaking into tears, as she had read the script and thus already knew about The Boss' ultimate fate.

The Boss's personal data (accessed via the radio during the Virtuous Mission) states that her hair is brownish gray, though her in-game character model actually has blond hair.

A voice casting sheet for Metal Gear Solid 3, which was leaked prior to E3 2004, stated that The Boss was a Green Beret and Navy SEAL, and that she was of British descent. These details were never mentioned in-game.

If the player picked up the magazine, still had it in their inventory, and called EVA shortly after leaving the prison area of Groznyj Grad, EVA, when questioned by Snake as to whether or not she threw any items away, will respond that she didn't throw anything away, not even the magazine that Snake had, referring to it as a "fine piece of literature" to Snake's embarrassment.

During the escape through the woods, if you interrogate EVA, there's a chance she'll say "Up, Up, Down, Down, Left, Right, Left, Right...", this is a reference to the Konami Code.

Major Ivan Raidenovitch Raikov's character is meant to mock MGS2's effeminate protagonist Raiden, who was met with mixed-to-negative criticism among Metal Gear Solid's western fanbase for replacing Solid Snake as the star. Although it isn't explicitly stated, the game heavily implies that Raikov is Colonol Volgin's gay lover.

This plays an important part during a particular scene when Snake is disguised as Raikov in order to infiltrate the Shagohod testing facility. Snake's cover is blown by Volgin who states that he was "waiting for Raikov in his room." Volgin grabs Snakes' crotch twice, thus revealing his identity. Volgin then exclaims "I know the Major better than anyone else." Volgin later beats Naked Snake to a pulp in retribution for Snake "hurting" Raikov.

Several other small hints at Raikov's sexual orientation are present in the game. If the player attempts to distract Raikov with a pornographic magazine, he will only give a brief glance at it and walk away instead of reading through it. Raikov also wears black underwear with a lightning bolt monogrammed on them (seen after stealing his uniform), a reference to Volgin's powers. EVA also drops hints about his homosexuality during a codec call.

MGS3: Subsistence later dropped more clues about Raikov. In the online mode of Subsistence, players can play Raikov, who's special move is a massive crotch grab that renders his opponent stunned. The Secret Theatre film 'Metal Gear Raiden: Snake Eraser' also jokes about Raikov's homosexuality and his purposeful resemblance to Raiden.

Despite being Volgin's male lover, Volgin himself appears to be bisexual, having an abusive relationship with Tatyana. He is a sadist, however, and treats her rather harshly compared to Raikov, whom he adores.

During the phone-call scene between President Lyndon B. Johnson and Premier Nikita Khrushchev, Johnson mentions that the Russians refer to The Boss as "Voyevoda."

"Voyevoda" is a Russian word for "warrior", "knight in training" or "leader of an organisation", and can refer to someone in the military or government with a degree of power. When used in regards to a female, it can also mean "lady knight." As Russia has had a number of famous queens in its history, this is considered a highly respectful nickname for The Boss.

Snake VS Monkey is a mode where the player plays as Solid Snake (judging by references to Otacon and Metal Gears as well as Snake talking with Campbell) wherein the player must catch the eponymous apes from Ape Escape. This mini-game was not included in the 3DS version or the multiplatform HD Collection, likely due to Sony's ownership of Ape Escape.

The Virtuous Mission take place in August 24, 1964. This date is also Hideo Kojima's 1st birthday. Kojima wanted to use his birth year, but moved that date forward a so that the Kennedy assassination could be included in the story.

In the "Health History" menu for Eva, it shows that she had procitis inflammation in the rectum, and also reveals that she had breast enhancement surgery.

Shooting Eva with the Mk.II Hush Puppy as she sleeps will cause her to mutter explicit things including "mmm, right there...", "Snake, that feels so good..." and a phrase referring to The Boss, "Boss, that feels so good..." She would also mention her dog.

A way to get the Single Action Army Revolver on the next playthrough is to choose the wrong gun in Snake and Ocelot's Russian Roulette duel.

While fighting The Sorrow, if you call people on the codec, they will speak as if you were at the death screen.

If you knock Ocelot out and then kill him, you'll get an automatic Game Over with an 'Ocelot is Dead' screen. You'll also be told, "Snake, you can't do that! The future will be changed! You'll create a time paradox!!"

If you wait for a few seconds after getting a Game Over, the text will slowly change from 'Snake is Dead' to 'Time Paradox'.

There is a way to kill The End before you even fight him. If you swim to a hiding place across from the Ponizovje Warehouse, you are in a perfect spot to snipe him. If you do kill him this way, Zero and the other support team members will congratulate you for killing him, although Snake will express disappointment in killing him in the manner that he did, as was hoping that he'd actually face him in battle. If you do this in the HD Collection, you will get an achievement called "The Early End."

If you enter the cure mode and rotate Snake for a while, he will vomit upon exiting the menu.

On the second disc of MGS3 Subsistence, there is a hidden "blooper reel" of alternate cut scenes. Most of them don't make any sense and are simply intended to entertain those who find them.

In Chinese, Big Boss's name is Tai Pan. Which can mean a foreign "Big Boss" or "Big Shot", but Tai Pan is also the name of one of the most dangerous families of the snake species in the world.

If the player saves their game at the beginning of their fight with The End, and then changes the PS2's internal clock to a week into the future, then resumes the fight, The End will have died from old age.

In the "Snake vs. Monkey" mode, you play as Solid Snake (unlike the rest of the game) and during the radio call in the beginning, Snake suggests that Sam or Gabe could take the mission. This is a reference to Sam Fisher and Gabe Logan of Splinter Cell and Syphon Filter, respectively. Splinter Cell and Syphon Filter were Metal Gear's two biggest competitors during its release.

When you fight Major Ocelot, unequip your weapon, and stand out in the open for a few seconds. A hidden cut scene will occur where Major Ocelot accepts your challenge, and comes out for a quick draw duel.

When you meet with Major Ocelot at Bolshaya Past Crevice, equip your Single Action Army Revolver, and begin to use the right analog stick to twirl the revolver. A hidden cut scene will occur where Ocelot will come out and twirl his revolver as well, and show off his freestyle tricks.

In Metal Gear Solid 3, you hear about a legendary sniper called "The End". He apparently can never miss a shot, will always kill his target no matter what from any distance, and without a spotter.

What isn't known is that his parrot is his spotter. If the player shoots the parrot in the battle, he has a harder time shooting you. He also becomes enraged.

If the player saves their game while in the Groznyj Grad jail cell after the torture sequence, Para-Medic will talk with Snake about the movie Dracula. If this save game is loaded, Snake will have a nightmare about a vampire, which is represented as a playable demo sequence of "Guy Savage", a cancelled Konami game.

In Metal Gear Solid 3, the Cobra Unit member "The Fear" uses a crossbow in battle and coats his bolts in the venom of the Brazilian wandering spider. Snake is hit with a bolt in a cutscene and The Fear describes the effects of the venom. However, one effect wasn't described by The Fear and wasn't displayed in the game at all. As well as causing intense pain, the venom has similar properties to Viagra, giving the victim an erection.