Easter Eggs are hidden secrets found throughout the Surgeon Simulator series.
- By putting in the red floppy disk, a game called Deep Dungeons of Doom (also made by Bossa Studios) can be played.
- A clock found in every mission and the main menu tells time in real-life.
- The watch worn by Nigel also tells real-life time.
- By inserting the black floppy disk (note: you need to complete Surgery and Ambulance modes to unlock this disk), you will be transferred by what is presumed to be the government into Space where you must perform a heart transplant. When the level starts, you unlock the achievement Spaaaaaaaaaace. The logo for it is Portal 2's Space Sphere or also known as the Space Core.
- By finishing the Meet the Medic DLC mission successfully, a small statue of the Medic will appear on the VHS tape player, and if you look on the bottom of this statue, there is a small taped-on note with a cryptic message. There is also some Korean writing which translates to "Time". This may or may not be linked to the strange update to Half-Life 2 on June 25th which caused all text and audio to turn into Korean. This could just be Bossa Studios playing a prank about the update, or it could be something larger. (NOTE: this was part of a ARG relating to the update Code-name: Trisha, it has been solved)
- As of Code-name: Trisha, you can now call her.
- Flipping the keyboard over reveals a message under it with links to the creators Twitter and Facebook: "Product Info: Surgeon Simulator 2013, Bossa Studios, www.bossastudios.com, Facebook: OfficialSurgeonSimulator2013, Twitter: @SurgeonSim2013".
- The achievement Stomach'O'Clock is a reference to Birgirpall's "I Broke Surgeon Simulator" video, when during the Kidney transplant Banzaii loses his watch and he asks what time it is, to which Birgirpall, his friend, says "it's Stomach'O'Clock".
- The achievement "Like A Wet Paper Towel" is a reference to Michael Jones and Gavin Free of Rooster Teeth's Achievement Hunters from their first Surgeon Simulator video in which Gavin lets go of the heart, making it fly away out of reach, causing Michael to get angry and yell at him telling him he threw it against the wall "like a wet paper towel."
- in Octodad: Dadliest Catch, you can find a board-game titled Nigel's Sturgeon Simulator Board Game.
- In Surgeon Simulator Touch if you try to break the patient's ribs with the radio it will change to the surgeon rap
- During any Ambulance Mode operation, the player can find a compartment on the right side of the ambulance with the words Sandwiches, cakes, and biscuits written on it.
- If the radio gets bashed around after the patient dies, such as might happen in an ambulance, the song will skip around and even play a few parts from the songs played in space.
- An achievement can be unlocked called 'Vworrrp Vworrrp', in which the player 'Creates a Timelord'. This is a reference the TV show, Doctor Who, in which the Doctor has two hearts. This can be unlocked during heart transplant, by putting the new heart in Bob before removing his old one.
- Pressing Shift+K will shrink or enlarge Nigel's hand.
- There is a secret message behind Nigel's Degree Plaque. It includes blank spaces (possibly for the secret code to unlock Gworb) and nine dots with a arrow pointing at the seventh dot (could be a representation of our solar system, if so, then the arrow is pointing at Saturn) a question mark, and Korean text that translates to "Time or It's Time". This used to be on the Medic Statue, but was moved to the Certificate later on.
- During the first Heart transplant surgery, if you poke the IV drip filled with blood on the right with a scalpel and drain it completely, there appears to be a bloody card inside the bag that says "09".
- In the eye transplant, hitting Bob with the plate will kill him instantly and make a "slap" noise.
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