X.A.N.A. has used multiple clones to complete his missions to defeat the Lyoko Warriors, destroy Aelita, escape from the Supercomputer, destroy the Supercomputer, and reclaim his lost source codes.
- A clone of Yumi Ishiyama that was used to lure the Lyoko Warriors to Lyoko and kill them. Appeared in Image Problem.
- While possessed, Jim Morales split into two clones of himself to fight Odd Della Robbia and Ulrich Stern. Possession occured in Final Mix.
- A polymorphic clone that was designed to cause distrust between the group by kissing other people, and then to kill Odd, Jeremie, and Yumi. Forms taken were Jeremie (Twice), Yumi (Twice), Ulrich (Twice), Yolande Perraudin, Aelita Schaeffer, Gilles Fumet, Suzanne Hertz, Jim, and Odd. Appeared in X.A.N.A.'s Kiss.
- A clone of Franz Hopper that was designed to gain the group's trust, but later kill them on Lyoko and steal Aelita's memory with the Scyphozoa, then suffocate Jeremie in Spectre form. Appeared in Franz Hopper.
- A polymorphic clone used to kidnap Odd, go to Lyoko, kill Ulrich and Yumi, and help the Scyphozoa steal Aelita's memory. Forms taken were Odd and Ulrich. Appeared in Revelation.
- A clone of Jeremie that was designed to send Aelita to Lyoko so the Scyphozoa could possess her and make her destroy the Mountain Sector, and kill the real Jeremie. Appeared in Double Trouble.
- A polymorphic clone that was designed to send Aelita to Lyoko so William Dunbar can throw her into the Digital Sea, and kill Odd, Ulrich, Jeremie, Chris Morales, and Jim. Forms taken were Chris and Jim. Appeared in Opening Act.
- A clone of an agent that was designed to send Aelita to Lyoko so William can throw her into the Digital Sea as well as damage the Supercomputer. Appeared in Crash Course.
- While possessing it, X.A.N.A. made Jeremie's Kiwi 2 robot multiply into a whole army that tried to kill Ulrich, Yumi, Jim, Sissi Delmas, Milly Solovieff, Tamiya Diop, Hiroki Ishiyama, Johnny, Jeremie, and Odd. Appear in Canine Conundrum.
- A clone of Jim designed to steal Ulrich and Odd's source codes. Appeared in X.A.N.A. 2.0.
- A clone of a little boy designed to steal Aelita, Yumi, Ulrich, and Odd's source codes. Appeared in Spectromania.
- A clone of Ulrich designed to steal Ulrich's source codes. Appeared in Spectromania.
- A clone of William designed to steal Yumi's source codes and chase after Ulrich. Appeared in Rivalry.
- While possessed, Remy split into three clones of himself to fight Yumi, Odd, Ulrich, and William. Possession occured in Suspicions.
- A polymorphic clone designed to steal the rest of Odd's source codes. Forms taken were the janitor, the gardener, and Samantha Suarez. Appeared in Countdown.
- A clone of (possibly) Theo Gauthier designed to hypnotize Yumi to give up the rest of her source codes. Appeared in How to Fool X.A.N.A..
- A clone of Anthea Schaeffer designed to fool Aelita into believing it is the real Anthea so it can steal the rest of her source codes. Appeared in Rendezvous.
- A clone of a football player that was used to steal the rest of Odd's source codes, and later to take Ulrich and Aelita's. Appeared in The Codeless.
- A clone of a bald man that was sent to Lyoko so Jeremie can steal back some of the source codes X.A.N.A. stole from Odd. Appeared in The Trap.
- A clone of Mrs. Hertz designed to steal Aelita's source codes. Appeared in Jeremie's Blues.
Jeremie Belpois' Clones
In season 4, Jeremie managed to succeed in creating clones just like X.A.N.A., though his' had personality malfunctions, such as his clone being athletic and social, and William's clone being stupid and easy-going.
- A clone of himself to ditch classes to work on freeing William from X.A.N.A.'s control, reconstructing Lyoko, and building the Skidbladnir. Ends up possessed by X.A.N.A. after William takes control of the Tower Jeremie was using to construct the clone. Appeared in Double Take.
- A clone of William designed to take the real William's place while the Lyoko Warriors worked on freeing him from XANA's control. Was once possessed by X.A.N.A. in Wreck Room. Destroyed after the team managed to free the real William in Down to Earth.