Following the January 20, 2016 update, the note within the game's files urging players to wait at least a year before posting sprites online was replaced by a new note reading "you know what i HATE? that's bepis THE TASTE the smell the texture hey.... your drooling......".

This is a reference to a man in Moonside from EarthBound who hates the food the player likes. Creator Toby Fox is a fan of EarthBound, and Undertale was heavily influenced by it. The word "bepis" itself is a slang term for "penis" that originated as a mispronunciation of the word and later evolved into an online meme.

In the game's demo as well as full version prior to patch v1.001, an unused song by the name of "grandpasemi.ogg" could be found in the game's files. This was likely intended for a cut character that could have been related to Sans, Papyrus, and possibly even W.D. Gaster, due to the name Semi being based on Semi Serif fonts. It is a short, slowed-down, and re-instrumentated version of the song Metal Crusher, which is used as Mettaton's first battle theme.

This same song is now used as of patch v1.001 when you deny feeding Temmie any Tem Flakes. It plays while Temmie makes a unique facial expression, with a text graphic appearing beside her that says "can't blame a BARK for tryin'...", immediately followed by Temmie trying to attack you with her extendable arm.

The game contains an unused battle with "RG 03" and "RG 04", which appears to be mostly complete with the exception of using placeholder graphics.

The song "Death By Glamour" is a remix of the songs "Core", "Metal Crusher", and "It's Showtime".

If you attack the dummy inside of the ruins, but attack and miss it nine times in a row, a text will pop up saying "Dummy tires of your aimless shenanigans." This will automatically end the battle, earning you 0 gold and 0 XP.

The song "Dating Start!" sounds almost exactly like the song "Turnabout Sisters" from Pheonix Wright: Ace Attorney

The song "Pathitic House" sped up sounds similiar to the song "Spider Dance".

During then credits after the Spoiler:pacifist run, if you dodge everything, yellow text will appear saying "Incredible work! Somewhere, felt a door opening...!". This unlocks a door in Snowdin Forest.

There are unused graphics of a robot NPC in idle and talking animation stored in the game's memory.

Naming the fallen child a certain name will give you unique messages after you chose it. Some names will also do certain things. Here is a list of names that give you unique messages and do certain things:

• Flowey - Message will say "I already CHOSE that name" and prevents you from using that name.
• METTA/METT/MTT - Message will say "OOOH!!! ARE YOU PROMOTING MY BRAND?"
• Alphys - Message will say "D-Don't do that" and prevent you from using that name.
• Alphy - Message will say "....OK????"
• Toriel - Message will say "I think you should think of your own name, my child" and prevents you from using that name.
• Sans - Message will say "nope." and prevents you from using that name.
• Papyru - Message will say "I'LL ALLOW IT!!!"
• Shyren - Message will say "...?".
• Asriel - Message will say "..." and prevents you from using that name.
• Napsta or Blooky - Message will say "............ (They're powerless to stop you.)"
• Frisk - Will initiate hard mode.
• Temmie - Message will say "hOI!"
• Aaron - Message will say "Is this name correct? ;)"
• Woshua - Message will say "clean name".
• Bratty - Message will say "Like, OK I guess".
• Catty - Message will say "Bratty! Bratty! That's MY name."
• Asgore - Message will say "You cannot" and prevents you from using that name.
• Gerson - Message will say "Wah ha ha! Why not?".
• Chara - Message will say "The true name". Removing the name from a save file will make the name be given by default.
• Gaster - Causes the game to go back to the intro, making the game not let you use that name without hacking.
• Bpants - Message will say "You are really scraping the bottom of the barrel".
• Jerry - Message will say "Jerry".
• AAAAAA - Message will say "Not very creative...?".
• Murder or Mercy - Message will say "That's a little on-the-nose isn't it...?".
• DrakGigiGugu - The item "Steak in the Shape of Mettaton's Face" will show as FSteak in the inventory instead of showing as Face Steak.

According to developer Toby Fox, the song "Redline Day" helped inspire him to make changes to the Undertale OST.

The game contains an ending error message where Sans will say;
"i'll be honest.i have no idea what happened for you to get here. this is actually some sort of error- handling message. so, if you're getting this ending...tell whoever made the game, okay? they'll fix it, or if it's a novel situation... they might even add another ending to the game. chances are, though... you're just a dirty hacker, aren't you? yeah, get outta here."

This works as an error handler when none of the available endings are triggered, which shouldn't happen during regular gameplay.

There is a mock up drawing of Omega Flowey (Photoshop flowey) showing that he was originally going to carry the souls rather than them being in his petals.

Attempting to name the fallen child "Gaster" will inexplicably reset the game. Spoiler:This ties into a subplot revolving around the unseen character Dr. W.D. Gaster.

A secret character who is hinted by people like the River Person is W.D. Gaster. According to clues scattered throughout the game, he was the royal scientist before Alphys and was responsible for creating the core, but he fell into the creation (which is implied to be the core, but could be the strange machine in San's secret workshop) and his life was cut short, disappearing from existence, but his consciousness is still present. Other than minor hints, trying to find W.D. Gaster and direct references to him can't be found playing the game normally, but can only be found if you edit the game's files and fun values. Also, if you go to your save file by editing the game files as well, you could also get a message from W.D. Gaster himself in the WingDings font (which is who he is named after), which he talks about his research, and then the game will crash.

Spoiler:There are two alternate ways that Muffet will spare the player. If the player fights Muffet through pacifist mode, and eats a spider doughnut in front of her. Or if the player buys either a spider doughnut or spider cider for 9999g.

Spoiler:Asriel Dreemurr's name is an anagram of "serial murderer".

The games files contain graphics for an unused "Doge" enemy.

Following patch 1.001, the unused audio file "abc_123_a.ogg", originally warning the player not to spoil the game online, was replaced with several text-to-speech voices laughing at the listener.

Napstablook's name may be a play on "Napster bloke," in reference to the file-sharing software Napster, which was frequently used to share music files. The computer in Napstablook's house also displays "a music-sharing forum".