- Beast/Hank McCoy, one of the original members.
- Cyclops/Scott Summers, one of the original members. He is the field commander of the X-Men.
- Gambit/Remy LeBeau
- Marvel Girl/Jean Grey, one of the original members.
- Jubilee/Jubilation Lee
- Storm/Ororo Munroe, second in command of the X-Men.
- Morph, was thought dead after a mission and was controlled by Mister Sinister. He rejoined the team but had problems with fighting again and left. He eventually came back once again after Xavier was injured.
After Xavier leaves with the Shi'ar it seems that Magneto made peace with the team and may have joined the team.
- Angel/Archangel/Warren Worthington III, one of the original members. He left the team for unknown reasons. Was briefly part of the Horsemen of Apocalypse.
- Iceman/Bobby Drake, one of the original members. He had problems with Xavier and left to be with his girlfriend, Lorna Dane.
- Lorna Dane, was a member when Iceman was there. They fell in love and left together. Later joined X-Factor.
- Professor X/Charles Xavier, the man who formed the team. He left the planet, and thus the team, when he was critically injured to be with Lilandra and the Shi'ar.
The X-Men originally were founded by Charles Xavier, who recruited Scott Summers, Jean Grey, Iceman, Beast and Angel. Moira MacTaggert was involved with Charles at this time and while being attracted to him, stated that she did not wish to be involved in the X-Men's training and left him, even though Charles plead for her to stay as he and the rest of the X-Men looked on. At some point after this, the X-Men had their first battle against Magneto, where Iceman was known to have attacked him. Lorna Dane joined the X-Men sometime after this as well and though they were interest in being members, Lorna was critically injured on a mission. This caused Iceman to regret his membership and leave the team, with Lorna choosing to leave with him as well. Angel left sometime after this and the X-Men received new costumes. Wolverine joined the team and was mistrusted by many of his teammate when he first arrived. Storm and Gambit joined as well, the latter said to have never been straight with the X-Men about his origins.
Rogue joined after having been contacted telepathically while still a member of the Brotherhood of Mutants. Morph joined the team as well sometime before or afterwards. Charles opted to help her with controlling her abilities and kept his promise. After this, Jubilee's foster parents registered her with the mutant control agency, a Sentinel attacked Jubilee at a mall before Cyclops, Gambit, Rogue and Storm saved her and took her back to the Mansion. After she left to make sure her parents weren't attacked, The Sentinels kidnapped her, hoping to find information on The X-Men. In the aftermath of the group saving her, Beast was captured by the humans and imprisoned while Morph was killed when he pushed Wolverine out of the way for safety. After the X-Men once again saved her, she joined them, realising it was the best place for her.
Wolverine, Cyclops and Storm had to stop Magneto from launching a missile. The three succeeded in stopping him. However, this lead Magneto to order Sabertooth to go after the team's base. Jubilee was left with watching after him and released him from his chains. He then threatened to kill her, she was without luck until Wolverine came to save her.
Scott and Jean went out on a date and encountered Morlocks, A group of mutants who had some type of disfigurement that led them to living in sewers. The two were captured and Storm, Gambit, Wolverine and Rogue came to their rescue. The four encountered the Morlocks' leader, Calisto. Calisto sought to make Cyclops her husband to help her rule the Morlocks.
Dealings with Spider-Man
Spider-Man originally came to seek Xavier's help with his mutation disease only to fight the X-Men and leave empty handed. After Beast went missing that same evening, Wolverine believed that Spider-Man set him up, and went gunning for the web slinger.
After realizing that Spider-Man wasn't to blame, Spider-Man and Logan searched for the real kidnappers, and found Beast's old colleague, Herbert Landon responsible. Landon had devised a plan to kill all mutants using Beast's earlier research.
After Spider-Man and Wolverine saved Beast, Landon fell into a vat of the mutant killing chemical and mutated into a huge, 30 foot monster. Spider-Man was forced to team with the X-Men and they managed to stop the creature. Wolverine then reminded Spider-Man that he didn't have to bare it all alone; he did have friends, and if he needed them, call.
When the Beyonder challenged Spidey to prove which is greater, good or evil, he chooses Storm to fight alongside him.
Days of Future Past
In one alternate future the X-Men, except for Wolverine, were all killed by Sentinels that had taken over the planet. Wolverine kept fighting but was captured by Bishop. Bishop was betrayed and Wolverine helped him go into the past to stop the assassination that caused it all. The graves of the X-Men served as reminders of the past and honored the fallen mutants. This timeline was erased when Gambit successfully stopped Mystique from assassinating Robert Kelly.
After stopping Kelly's assassination Bishop returned to the future where all the X-Men, including Wolverine, were killed by a virus. Logan's skeleton was studied by a version of Forge. Forge told Bishop, who had no knowledge of this world, about the virus and he went back in time again to stop it. This version was erased after Cable spread the virus to Wolverine so he could create the necessary antibodies to survive.
Trevor Fitzroy, under the orders of Master Mold, traveled back to 1959 to kill Xavier. He succeeded and Xavier's friend Magneto formed the X-Men in his honor. However, anti-mutant sentiment turned violent and war spread throughout the world. Storm and Wolverine were romantically involved and married. When the X-Men were engaged in a battle with this world's Avengers Bishop and Shard arrived from their time. They took Storm and Wolverine back in time to stop Fitzroy. Wolverine was hesitant to help as he did not know if he and Storm were involved in the normal timeline, but Storm convinced him to help. They initially failed in their attempt but went back once more and succeeded. This timeline was erased as it reverted to normal. Xavier's memory of Storm and Wolverine is the only remnant of this timeline.
Angel's appearance in several flashbacks conflicts with his early appearances in the series, as the other X-Men do not seem to recognize him despite apparently knowing him already.
Various other mutants who have officially joined the team in the comics but not on the series were seen. These included: Mimic, Polaris, Havok, Nightcrawler, Banshee, Sunfire, Colossus, Thunderbird, Rachel Summers, Psylocke, Dazzler, Longshot, Forge, Bishop, Cannonball, Cable, Emma Frost, Northstar, Paige Guthrie, Juggernaut, Warpath, Hepzibah, Caliban, Karma, Moira MacTaggert, Deadpool, Mystique, Sabretooth, Warlock, Illyana Rasputin, Wolfsbane, Sunder, Multiple Man, Strong Guy, X-Man, Frenzy, Forearm, and Namor.
Magneto has joined the team several times in the comics but it is not directly stated if he did so at the end of "Graduation Day".