Warning! Contains spoilers for The Marvels While the the MCU movie timeline, has introduced hundreds of characters from the Marvel universe to help flesh out their interconnected multiverse. However, back when Marvel Studios was still fresh, they didn't have access to significant characters like Spider-Man, the Fantastic Four, and the X-Men. Before Disney acquired 21st Century Fox, the word "mutant" could never even be said in a Marvel movie or TV show (let alone referencing the X-Men), and characters that both studios shared had access to had to be retooled for the respective universes.
However, things have changed for the better, as the Fantastic Four and X-Men rights have come into Marvel Studios' possession. There's no concrete news on Multiverse Saga timeline.

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15 Wolverine's Weapon X Connects To Captain America
The Incredible Hulk (2008)
The MCU's first X-Men reference was a blink-and-you'll-miss-it nod to Wolverine's past in early franchise black sheep, The Incredible Hulk. In the second MCU movie, Thunderbolt Ross's (William Hurt) plan to capture the Hulk see him give Emil Blonsky's (Tim Roth) a modified version of the Super Serum formula, creating The Abomination. A closer look at the villain's origin sequence reveals that the serum was produced by Stark Industries in conjunction with Dr. Abraham Erskine (Stanley Tucci). Most interestingly, the experimental program is revealed to have been called "Weapons Plus", the same one from Marvel Comics that gave Wolverine (Weapon X) his iconic Adamantium exo-skeleton.
14 Dr Erik Selvig's Research Reveals The Fault
Thor: The Dark World (2013)
2013's X-Men Easter egg the Fault.
In the comics, the Fault is tied to a major X-Men tory event. After the war between the Kree and the Shi’ar Empire, led by Vulcan (the mutant brother of Cyclops and Havok), a rift in space was created in a battle between Vulcan and Black Bolt. That breach in space then introduced the so-called Cancerverse to the Marvel Universe, which is a reality where the concept of death had been defeated. So far, the MCU has not mentioned the Cancerverse explicitly, however, the mention of The Fault did allow Marvel Studios to give the fans one of its earliest hints at the MCU Multiverse. But it also served as something related to the X-Men comics without specifically mentioning mutants.
13 The Maximoff Twins Have Special Genetics
Captain America: The Winter Soldier (2014), Avengers: Age Of Ultron (2015) & The Wakanda Files (2020)
In Marvel Comics, Scarlet Witch and Quicksilver are revealed to be the children of X-Men veteran villain Magneto. Obviously that wasn't possible in the MCU, given Fox's ownership of the necessary character rights, but that doesn't mean they couldn't be mutants. In Captain America: The Winter Soldier, the twins - played by Elizabeth Olsen and Aaron Taylor-Johnson - were introduced as Hydra guinea pigs as part of experiments on the Mind Stone. Many test subjects were killed, but Wanda and Pietro survived, gaining extraordinary superpowers they would debut in Avengers: Age of Ultron a year later.
The mystery of why they weren't killed and instead gained powers came in 2021's Wakanda Files - an in-universe book written by Shuri, which explained that the Maximoffs had genetic markers that suggested latent superpowers. In other words, they were as close to mutants as the MCU could ever say.
12 Mysterious Lightning Strikes In The 1970s Hint At Storm
Avengers: Endgame (2019)
As Steve avoids being seen, he overhears Peggy talking with another agent about "Braddock's unit" (a Captain Britain reference) being stopped by lightning strikes. But Peggy goes on to say that it's not the lightning strikes they're looking at, after having reviewed the weather projections, alluding to one of the most popular X-Men of all time: Storm. While the MCU got to name-drop Captain Britain himself, it does seem that they also teased Ororo Munroe's existence.
11 Mutant Sanctuary Madripoor Comes To The MCU
Falcon & The Winter Soldier (2021)
One of the locations in Madripoor X-Men connection is undeniable, as it's a location that has appeared in various X-Men stories. One of the notable Madripoor-based X-men stories saw Wolverine tryd to hide from the world and make a new identity when society believed all mutants to be dead. Perhaps there are several mutants who live there currently that the MCU may revisit down the line.

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10 Evan Peters' Quicksilver Returns... Sort Of
WandaVision (2021)
While Aaron Taylor-Johnson played Quicksilver in WandaVision season 1, episode 5, "On a Very Special Episode…," Peters makes a surprise appearance in Wanda's manipulated Westview as a "recast" version of Quicksilver.
Even though Peters playing Quicksilver meant something more to the audience than Wanda, it turned out that he wasn't actually taking over for Taylor-Johnson. It was a bait-and-switch, and one not all fans appreciated. Rather than being the real Quicksilver, he was actually revealed to be an imposter who had been put under a spell by the Katheryn Hahn's Agatha Harkness. In reality, he was an aspiring actor by the name of Ralph Bohner. It was disappointing to some fans that this wasn't the MCU bringing Peters' version of the character into canon. However, it was still neat of WandaVision to use it as a wink to the audience from the X-Men movies.
9 Professor Charles Xavier s The Illuminati
Doctor Strange in the Multiverse of Madness (2022)
Even though Evan Peter's "Quicksilver" turned out to be a controversial bait-and-switch, it wouldn't be long before a real mutant showed up in the MCU. Thanks to the creation of the Multiverse, audiences have seen alternate universes within the MCU. As revealed in Doctor Strange in the Multiverse of Madness, some clearly already contain mutants. This is how the MCU introduced its first confirmed on-screen mutant – Professor Charles Xavier (Professor X) of Earth 838.
Unlike the WandaVision Quicksilver appearance, this is confirmed to be the same Professor X who founded the X-Men and vowed to find a way to bring peace between humanity and mutantkind. It should be noted that he doesn't implicitly say the word "mutant," but shots of the X-Mansion were cheekily included in early Doctor Strange 2 trailers. This Charles Xavier is a member of Earth 838's Illuminati, and to make doubly sure audiences know he is indeed Professor X, the famous X-Men 97 intro riff plays when he makes his appearance. He's even riding in the same yellow hoverchair made famous by the original animated series in the '90s.

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The Charles Xavier of Earth 838 is shown to have the same incredible telepathic abilities as his comic-book and Fox movies counterpart. Sadly, his powers aren't on par with the Scarlet Witch, however, and Wanda makes short work of Professor X by psychically snapping his neck. It's fitting that Professor X would be the first mutant to appear in the MCU, being the founder of the original X-Men. Whether the MCU Earth 616 has its own Charles Xavier isn't yet known. However, as of Ms. Marvel, the MCU does have its first Earth-616 mutant, without any Multiverse variants or Agatha Harkness trickery to be seen.
8 Kamala Khan's Gene Analysis Results Make Her A Mutant
Ms. Marvel (2022)
In the finale of Kamala Khan's powers was finally revealed – and she's a mutant. In Episode 6 of the Disney+ series, Kamala has Bruno investigate her origin and, most importantly, her genetics. What he says when he delivers his findings could possibly be one of the most important moments in the MCU so far. He tells Kamala he's spotted something that makes her different from her family, "like a mutation." It's the first time a character in the MCU has used the M-word and confirmed that mutants exist in the MCU.
Now, this choice of words could have been deliberate fan bait. Marvel has been accused of doing this before, such as when Evan Peters showed up as "Quicksilver" in Wandavision. As if to make sure audiences knew the studio had learned its lesson, however, when the Kamala-Mutant reveal is made, the X-Men 97 riff that appeared alongside Professor X in Doctor Strange 2 is played. This is almost as clear an indication possible that Kamala's mutation is the same kind that earns one entry into Xavier's School for Gifted Youngsters (if such a place exists in the MCU yet).
This isn't only significant because it introduced its first official mutant. In the comics, Kamala Khan is an Inhuman. Ms. Marvel's Inhuman origins have always been pretty central to her character, too. It was one thing for the Ms. Marvel MCU series to break away from her being an Inhuman, but it's another step entirely to retcon a distinctly non-mutant character into a potential X-Man. Inhumans and Mutants are different in the comics, so much so that the hypocrisy of anti-mutant sentiment not extending to Inhumans is a theme of more than one book. Marvel even tried using Inhumans to downplay the prominence of the X-Men in popularity, back before Disney/Marvel Studios owned the license to the property. Kamala Khan making the jump from Inhuman to mutant is perhaps their biggest break from comic-book canon yet. It also opens the door for other characters being granted mutanthood within the MCU that never possessed an X-Gene in the comic books.
7 Hulk Always Had Latent Superhero Genetics
She-Hulk (2022)
Like the Maximoff twins and Ms. Marvel before him, Hulk was revealed to have genetic markers that made his superhero origin possible years after his debut. In She-Hulk: Attorney at Law episode 1, Mark Ruffalo's Bruce Banner reveals that he and his cousin Jennifer Walters share "a rare combination of genetic factors" allowing their bodies to synthesize Gamma radiation. That in turn suggested that those genetic anomalies were the reason they survived exposure to Gamma radiation. In other words, they possessed a mutant gene that meant they didn't die during their transformations in Hulks.
6 Wait, Wolverine Exists Already In The MCU?!
She-Hulk (2022)
The MCU dropped several Wolverine hints in other MCU projects prior to the announcement of his return in Deadpool 3. Most notably, an Easter egg in She-Hulk: Attorney At Law saw a news headline mention a man with metal claws taking part in a bar-room brawl. While metal claws could reference a number of Marvel characters, its appearance so close to the Hugh Jackman Deadpool 3 reveal means there's a strong chance it was a reference to Logan himself.
Later in the same season, Nikki Ramos (Ginger Gonzaga) jumped out from behind a wall, with makeup brushes between her fingers, and saying “snikt.” For all Wolverine fans, that sound effect links directly to Marvel Comics' berserker when he extends his claws. Quite how Nikki knew the reference is unclear, even with She-Hulk's fourth wall and universe-breaking finale.