Version Differences

PAL JP mill box — larger box in PAL and JP

Nintendo logo in JP

The developers made some changes to the game between its regional release dates. Since several time-saving glitches were removed, it is highly recommended to use the US version for speedruns.

These are all known versions of Donkey Kong 64:

NTSC-U, aka US/NA: North American version, released on November 24, 1999
PAL: European/Australian version, released on December 6, 1999. Wii U Virtual Console release on April 2, 2015
NTSC-J, aka JP: Japanese version, released on December 10, 1999

US Differences[]

Speech bubbles can display six lines of text at once.
Phase Swimming was fixed in PAL and JP.
- Since Phase walking & Phase falling abuse the same bug as Phase Swimming, these are also patched in PAL/JP too
In PAL and JP, Swim Through Shores is notably harder on fairy island.
DK can roll into the square platforms near K. Lumsy's prison. This does not work in PAL and JP, as invisible walls keep you from clipping.
Inside the mill in Fungi Forest, you can walk through the gap between a beam and a box near the Mini Monkey entrance using DK, Chunky or Lanky. For the later versions, the box was extended to the right side, which removed the gap.
If you charge up the shockwave attack with Chunky, walk up to a boulder and release B while it's in mid-air, Chunky will be holding an invisible rock. This also freezes the game sometimes. In PAL and JP, he loses the invisible rock immediately so the game can't freeze.
The banana medals in Hideout Helm will be grayed out forever if you don't collect them before leaving. This was fixed in PAL and JP.
The propellers on K. Rool island and inside Snide's H.Q. were changed from red to blue in PAL and JP.
A person called L. Godfrey was removed from the Rare Testing part of the staff roll in later versions of the game.
If you interrupt the End Sequence and watch it again, the text will continue from where it left off and eventually start from the beginning. Right before that, the number 33 will be displayed.
Backflipping and moving Diddy in a certain spot can make Diddy clip through the bridge in the mountain in Jungle Japes to access the switch (which spawns the GB) faster. This is significantly harder on PAL/JP
Chimpy Charging into the left arch upon entering Tiny Temple can clip you through, enabling you to access the Free Tiny room and her GB without melting the ice. This was patched on PAL/JP as they added a wall there
Backflipping into where the Troff 'n' Scoff portal was (near Cranky's in Galleon) will enable you to clip out of bounds whilst gaining some additional out of bounds height. This is patched on PAL/JP
On PAL/JP, when you defeat Fungi Boss, you get a small punch sound effect for the final punch. This doesn't exist on the US version
By doing certain trickery with first-person, you can enter the swimming animation without completing dive barrel on the US Version (More commonly known as a 'Pseudo-dive'). This is patched on PAL/JP
In Fungi Forest, the Troff 'n' Scoff portal alcove near the Giant Beanstalk is shaped like a pentagon on the US release. On PAL/JP, it's shaped like a rectangle
Going under surfaces which cause insta-death (eg. Lava in Helm Lobby, Acid in Creepy Castle Lobby) will cause an instant upwarp to y=999,999 on the US release of the game (On N64, this would cause a crash). On PAL/JP, this bug is fixed.
Storing the Pineapple Switch in DK Isles, and then entering the Fungi Cannon would launch the kong incredibly high on the US release. The y value peaks at around 44,850.
It is possible with usage of Hunky Chunky to clip through the shell in Jungle Japes due to poor collision. This is patched on PAL & JP
The slope inbetween the vines & Funky's Armory in Jungle Japes is heavily solidified on PAL/JP, making it signficantly harder to clip through it

PAL Differences[]

US and JP run at 60 Hz and ~30 fps, but PAL runs at 50 Hz and ~25 fps, which is 1.2 times slower. However, the lag compensation speeds up the kongs so they move as fast as in the NTSC versions. Everything besides movement (cutscenes, menus, enemies, ...) is slower than in NTSC.
Speech bubbles can only display four and a half lines of text at once due to greater line spacing.
US and JP are English or Japanese only, respectively, whereas PAL has a language section in the options menu that features English, Spanish, German and French.
The part of the Forest boss intro cutscene where Chunky bows in fear was cut out.
The staff roll features German, French, and Spanish Translators as well as NOE Testing.
Upon landing on the ground from entering a cannon on US/JP versions of the game will give you control early enough that you can hold Z to cancel the animation of getting up (Which saves time). However, you don't gain control as early on PAL, and therefore cannot skip the animation.
In the US/JP release, by using Swim Through Shores, you can jump under Tiny's Caged Banana in DK Isles to skip the dance whilst remaining out of bounds. On PAL, it's significantly easier to clip through the floor meaning you're stuck in the cage unless you pause/exit or clip out. In MMM, this would likely result in a softlock.
On PAL, you are given 2:30.00 (In-Game Time) per K Rool Phase as opposed to 3:00.00 (In-Game Time) on the US/JP releases. However, the text at the start of the K Rool Fight from Microbuffer about the length of the phases remains unchanged ("Twelve Three-Minute Rounds")
Storing the Pineapple Switch in DK Isles, and then entering the Fungi Cannon would launch you to exactly y=8192 on the PAL release before falling.
The poles in Tiny Phase are considerably harder to climb on top of compared to US/JP
On PAL, you can clip on the torches in the 3rd area of the Jungle Japes Shellhive. These clips are not possible on US/JP without lag assistance

JP Differences[]

The speech bubbles are bigger and can display seven and a half lines at once.
Speech bubbles can't be canceled with B, but their text shorter and you can still hold A to speed it up.
The Nintendo logo at the start is white, as opposed to the red one in US and PAL.
A different font is used for white text.
The title screen shows the Japanese translation of Donkey Kong (ドンキーコング) below the game logo.
The text on the signposts inside DK island is Japanese.
The trigger zone for the Diddy cutscene in Japes was moved 75 units towards the tunnel, making the standard cutscene skip impossible. However, you can use orange lag to increase your kick distance and still reach the warp pad.
You can swim through a spot at K. Rool's ship where several polygons meet in order to get to Gloomy Galleon. The collision detection on that spot was fixed.
The ground next to the slanted wall on the llama temple was changed in a way that makes you slide off of it. In order to clip inside the temple you would need to fly into that wall at a specific angle, which is significantly harder than the C-up or orange clip.
When you first enter Troff 'n' Scoff's room, the speech bubble shows up a few seconds later than in US and PAL. This prevents a softlock that occurs if you play in a duped file and the boss door is already open.
If you interrupt the End Sequence and watch it again, the text will continue from where it left off and eventually start from the beginning. Right before that, a line of Japanese text will be displayed.
Storing the Pineapple Switch in DK Isles, and then entering the Fungi Cannon will carry out the traditional Cannon shot path whilst the cutscene plays in the foreground for JP.
The Japanese version saves the fact that the gate at the start of Jungle Japes (opened by 2 peanut switches) has been opened through pause exit and resets, the US and PAL versions do not.
The Hunky Chunky Barrel in Aztec is considerably higher on JP.
This also applies to the Hunky Chunky Barrel in the Giant Boulder Room in Caves.
After turning in all 40 Blueprints, Snide will give you an additional piece of dialogue: "Mission completed. Thank you kong. Well, let's spook K.Rool!". This text only appears on JP.
The Golden Banana inside the box in Frantic Factory's dark room isn't grabbable until you break the box on JP.
The torch opposite to the entrance in Tiny Temple is further away from the wall on JP compared to US/PAL. As a result, a push cannot be performed on JP
Chunky can use swim through shores on some walls in some levels to clip out of bounds, otherwise known as the 'Chunky Dunky'. This is not possible on JP
There is a weak wall to the right of the entrance of Chunky's 5 Door Cabin in Crystal Caves that you can clip through relatively easily. This wall is nowhere near as weak on JP.

Differences between US v1.1 and JP[]

The US v1.1 (Otherwise known as the LodgeNet version) was only available using the LodgeNet system. LodgeNet was a system which allowed customers to play Nintendo 64 games in hotel rooms at the cost of $6.95 (plus tax) per hour of gameplay. The version of Donkey Kong 64 that was on LodgeNet was built roughly 2 weeks after the Japanese version so mostly reflects the JP version. However, there are some key differences which make the LodgeNet version incredibly unique.

It's worth noting that v1.1 was never ported to Wii U VC. The US Wii U VC ROM is US v1.0.

Text is in English and allows for text skipping. Additionally, the font used for the DK Rap and Hideout Helm timers is the same one used for the US 1.0 and PAL releases.
The Intro Story cutscene upon starting a fresh file with "story skip" off can be skipped by pressing either the START button or A. Upon doing so, it'll warp you to Training Grounds outside Treehouse, which is where you spawn if you had story skip on. Unintentionally, this feature also works with "K. Rool Press Button" (Only the portions of the cutscene which take place after the Helm segment) and "K. Rool Takeoff", which also warps you to Training Grounds upon skipping.
On the file percentage screen, a piece of text appears on the bottom which reads "TRAINING ON". This can be toggled to "TRAINING OFF" by pushing left or right on the control stick on the file percentage screen. If you set this to "TRAINING OFF", you will start your file with all 4 training barrels and simian slam, skipping roughly 2.5 minutes of gameplay.
The LodgeNet system only supported 1 controller. As such, the game blocks access to kong battle with no way around it. This technically patches some ISG-based glitches like Funky Weapons Glitch.
Pressing up and down on the DPad will get the game stuck in a while-loop, effectively pausing the game until you press left and right on the DPad. Up/Down or Left/Right have to be input on the same frame, making this very hard to do on an N64 controller without wearing the DPad down. It's theorized that the LodgeNet system would use this pause functionality once your paid time with the game was up, and to allow the player to spend money to get more time, with the LodgeNET system sending the inputs to the controller. The developers of DK64 forgot to account for lag boosting, so this pause feature can be abused to lag boost to an arbitrary degree

Wii U Virtual Console Versions[]

The Wii U Versions of the game mostly represent the original N64 versions (US/PAL/JP), however, there are some notable differences that are applied to each version on top of the original patches stated above:

The Wii U VC versions lag a lot less than the Nintendo 64 versions. This makes certain tricks which are lag-assisted (to some degree) harder. It also makes AI move a lot faster since the AI's calculation rate is drastically increased. This means that boss fights are quicker, but the Rabbit Race in Fungi Forest is harder.
Successful fairy pictures can be taken through walls
Going to extreme y values in both directions will crash the Nintendo 64 (Somewhere in the realms of +/- 50,000). This is mostly evident with the Fungi Cannon Shot glitch (US) and Lava Upwarp (US), which both crash on Nintendo 64. Performing these glitches on Wii U will not crash the game.
The Virtual Console emulator has a savestate function built in. The most this impacts though is allowing for faster resets of speedruns and consistent Main Menu Moves without file examination
The Sir Domino enemies appear with a green tint around them instead of purple.
Audio skipping and missing audio channels is more common on the Virtual Console.
The Troff 'n' Scoff for DK Isles does not crash the game on Virtual Console (unlike N64).
- However, unlike 3rd party N64 emulators (which also don't crash upon attempting to enter Isles Troff 'n' Scoff), the Virtual Console Troff 'n' Scoff for DK Isles is riddled with invisible walls, ceilings and void triggers. This makes accessing the boss door loading zone (which takes you to K Rool) very tough.
When a game code instruction would result in an exception (eg. Converting NaN between float formats), the Virtual Console ignores the game instruction (unlike N64, which would not ignore the instruction, and would likely crash). Due to this way of handling exceptions, adverse effects are often caused when replicating N64 crash situations on Virtual Console.