Fantomex has with three brains for independent parallel processing, and 'nano-active blood'. Fantomex's primary nervous system is actually a detachable techno-organism called E.V.A. After being killed, he was cloned in a way that his three brains each received a body, leading to the existence of Fantomex, Cluster and Weapon XIII. Later, the clones were reabsorbed back into his original body.

Fantomex possesses a secondary, internal nervous system that he can activate to prevent negative feedback from E.V.A., but its functions are limited, allowing him to see only in black & white.

Fantomex can place himself in a trance-like state to recover from injuries. In this state he has been known to forcibly expel bullets and recover faster while placed in water.

Fantomex has displayed superhuman agility and enhanced strength.

His body doesn't create any scent, making it difficult for even the likes of Wolverine to track him.

Former powers he possessed were:
E.V.A.: an autonomous picotoch entity manifesting his primary nervous system externally, with retractable landing legs, hovering and propulsion capabilities, morphing doorways, passenger room, and a machine consciousness. He could see through E.V.A.'s point of view and could take control of her movement. However, this required extreme concentrations on the part of Fantomex. Moreover, E.V.A could fly "herself" and generate bio-electric charges to be used as weapons. Fantomex was both telepathically and symbiotically linked to E.V.A. As a result, whenever E.V.A. was traumatized or injured, Fantomex experienced the same pain.

While separated, Fantomex felt no pain and seemed able to ignore most injuries.

Fantomex - when working in conjunction with E.V.A. - had the ability to 'misdirect' another person, including the use of illusions. Together, their combined consciousnesses could create extremely convincing illusions. It seemed even powerful telepaths could not truly tell if he is lying or not. This includes misdirecting someone's feelings.

Fantomex showed he could eject E.V.A. as a ball of bio-electrostatic energy that can shock and immobilize enemy designates through the usage of her onboard picotech.

After having pirated and copied Hope Summer's affliction who in turn copied the fatal chemical augment from her stricken father, Fantomex managed to fabricate a digitized version of what ails them both and rewrite it into only enabling him use of it's empowering effects without self-destructing in due time but also bestow and develop whole new powers on the fly onto himself whenever he pleases.

Fabricated a pair of jet black aerial extremities resembling those of a former comrade after having re-purposed the Surrogate Phy/Psi. Nervous System as Doctor Nemesis calls it, beyond being able to use them as razor blades due to near monomolecular sharpness coupled with the discharging of razor flechettes.

Self-Propelled flight

Having been ported into the sun itself and making it back to earth within mere moments showcasing he has escape velocity to virtual light speed motion.

Showing he could take a bullet to the head and recover in a matter of minutes including tank a bomb blast to the face and shrug it off with ease. Even once being teleported into the surface of the sun while not even being slightly singed by it on top of being sliced to ribbons by a frenzied marrow and then blown apart by massive explosion only to have his scattered bits culminate in order to rebuild himself once again.

First manifesting this capability shortly after getting shot behind his skull, he lashes out with countless energized tendrils similar to Volga when he first appears before X-Force. After time and practice he shows to control and discharge various other energies in the form of fire balls or plasma.

Fantomex could discharge potent quantities of red energy from various points of his body at will.

Fantomex was briefly able to create force fields.

Fantomex was shown to be able to shift size at will.

Fantomex had enhanced strength and durability.

Fantomex used a form of biological absorption to assimilate one of Cable's many clones into himself.

He speaks English. He often uses French words and a French accent, but in fact doesn't speak french.

Fantomex referred himself as a mutant/sentinel dichotomy, seemingly feeling himself both, at least symbolically.

He was later among the mutants dragged into Legion, although similar argument has also been rejected as an artist error for Puck being raptured by the Scarlet Witch.

When joining Cable's X-Force in X-Force Volume 4, he was stated to be a mutant.

Developed by the Weapon Plus Project both for use as an agent and as a potential prototype for the next generation of "Super Sentinels", he has been classified as many things: Human mutate/cyborg, mutant, and Super-Sentinel.

Originally three-brained with mutated autonomous External Nervous System; Later the embodiment of only one of those brains.