The Erie County Medical Center in Buffalo said in a statement Friday that the cancer was found when the former Buffalo Bills star came in for follow-up testing after having oral surgery to remove cancerous cells last year.
The statement says the hospital's head and neck cancer specialists are determining a course of treatment.
Kelly spent 11 seasons with the Bills before retiring following the 1996 season. He has since made Buffalo his home.
The hospital says Kelly asks that people keep him and his family in their thoughts and prayers.
His son, Hunter, was born with Krabbe (KRAB'-ee) disease, an inherited nervous system disorder. Given little more than three years to live, Hunter died at the age of 8 in 2005.