Charles Xavier is one of the world's premiere experts on mutants. A mutant telepath, Charles and his wife Moira MacTaggert wrote the book on post-human medicine, treating young mutants endangered by their own powers. Their mutant son David was born a few years into their marriage, but Charles never felt close to him. He had a strong bond with Erik Lensherr, the first adult mutant he ever met. As Charles and Moira drifted apart, Charles abandoned his family and helped Erik establish the Brotherhood of Mutants. Charles gradually realized Erik, now calling himself Magneto, didn't share his goal of peaceful coexistence with humanity. When Charles and his allies fled the Brotherhood, Magneto impaled Charles with a metal spear, severing his spine.

As the Brotherhood turned to terrorism, Charles worked to oppose them. Offered funding for a mutant school and hospital by the Hellfire Club, Charles asked Moira to take charge of the latter, ensuring that his sickly son David had constant treatment. At some point, Charles romanced his adult student Emma Frost, who eventually left him after arguing against what she viewed as plans to turn his students into soldiers. When the government launched the robotic anti-mutant Sentinels in response to the Brotherhood's terrorism, Charles sent his new students, the X-Men, to save mutants from the killer robots. The X-Men rescued the President's kidnapped daughter from the Brotherhood, winning Presidential favor, which was augmented when they saved Washington from destruction and Charles apparently slew Magneto. Charles secretly spared Erik, rendering him an amnesiac in the hope of eventual rehabilitation.

When David went on a murderous rampage, Charles found himself unable to kill his son, so Colossus, one of his X-Men, did it for him. Feeling himself a failure for letting down both David and his student Iceman (whom David hospitalized), Charles nearly disbanded the X-Men. Apparent progress with Magneto's rehabilitation convinced him to persevere. Tragically, Magneto later regained his memories and returned to terrorism. Suspected of collusion because he had lied about Magneto's demise, Xavier was captured by the Ultimates and imprisoned in Camp X-Factor in Guantanamo Bay. Later freed in a Brotherhood raid, he coordinated efforts to contain a nuclear power plant meltdown Magneto instigated, publicly redeeming himself. The X-Men were allowed to continue under S.H.I.E.L.D. jurisdiction.

Xavier is sometimes accused of using his powers to influence people for his own ends; though he denies this, he is not above deceit and manipulation. In his own way he is just as fanatical as Magneto. Only his conscience prevents him from being just as ruthless in the pursuit of his goals: protecting his students and achieving mutant-human coexistence.