While Loki studied the real O'Neill, his clone was to take his place on Earth for one week's time. For O'Neill's own protection, the Asgard had placed a marker in his DNA to prevent any attempts in genetic manipulation. Loki, not realizing this, duplicated O'Neill nevertheless -- and as a result, the clone was rapidly matured only to about age 15, instead of the Colonel's actual age.
The duplicate, not realizing he was a clone, went to the S.G.C. looking for answers, and soon discovered a flaw in his DNA that was going to kill him. At O'Neill's request, Thor repaired the genetic defect. The Air Force took O'Neill's young clone under their wing to provide for his future, and he returned to high school to live his adolescence over again.
Fragile Balance - The Asgard Loki clones Jack O'Neill, replacing the real Colonel with a teenage version of himself for one week. Young Jack refuses the Tok'ra's offer to cryogenically freeze him when it's discovered that he is dying of a genetic flaw.