- A chapter in The Arctic Incident called Mulch Ado About Nothing is named after the William Shakespeare play, Much Ado About Nothing.
- Book Six, and Artemis is playing the defense. Cue "'But this creature is magical', objected Artemis, banging the podium with his fist"
- There's also Artemis' little brother Myles who seems overly fond of his father's cravat...
- Again in Book Six, Mulch talking to Opal Koboi. "I bet you would set the world on fire just to see it burn." What's really weird is that this shows up in the U.S. copy of the book, which was released over a week before the premier of The Dark Knight. Considering how long the editing and publication process takes, this is most likely not a shoutout, just a coincidence.
- In Opal Deception, mind-wiped Artemis wakes up and sees Holly (whom he no longer recognizes) sitting next to the bed crying.Artemis: Why are you crying, girl?
- Lampshaded in Book seven:Artemis: "The lives of many are more important than the lives of the few."Mulch: "I saw that on Star Trek."
- In Book Seven, Mulch mentions a "program about an angry, foul-mouthed chef and his staff that he enjoys watching,"
- Juliet using a roundhouse kick to take out a bearded cowboy.
- A chapter named Murder Most Fowl from the Time Paradox is also the title of a book. There's also two references to The Lord of the Rings in the same book. 'all real, just like Lord of the Rings' and 'like one of Tolkien's creatures'.
- Artemis also uses the alias Stefan Bashkir, the same name as Stefan from one of Eoin Colfer's other books, The Supernaturalist.
- Chapter sampling from the second book: To Russia With Gloves, Mulch Ado About Nothing.
- Three of Commander Root's cousins were in the movie of The Wizard of Oz.
- Af books have several references to great criminal of older date Jim DiGriz most obvious are
- book 5 - where Artemis returned from time travel several years later than he came and find his mother Angeline has twins
- book 2 - When Artemis use his blood to fake shooting his father.
- Foaly tells his nephew Mayne in the last book, "Listen, nephew, if you want to strap a horn to your forehead and go to conventions on the weekends, that's completely fine" and references a miniseries about unicorns that Mayne is rather obsessed with. Seems the Lower Elements have their own version of My Little Pony: Friendship Is Magic.
- That, or Star Trek, since Mayne also speaks "Unicornian", an In-Universe fictional language (compare this to fans of Star Trek speaking Klingon).
- In the final book, Foaly pokes fun about the fear of the number four Artemis had while suffering from his Atlantis Complex by telling him "May the fours be with you."
- Two companies crossed over between the Artemis Fowl series and The Supernaturalist
- Phonetix: originally mentioned in Eternity Code as the main competitor to Jon Spiro's Fission Chips
- Krom Automobiles: originally mentioned in The Supernaturalist makes an appearance in Last Guardian as a fairy company that bought the former Koboi Labs building.
- When Mulch breaks into the actress's apartment in the Arctic Incident graphic novel it's done in a similar style to Rorschach entering The Comedian's apartment at the start of Watchmen, including a billboard advertising a candy called Mmeltdowns.
Shout Out / Artemis Fowl