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.