Kilgallon was out of contract at the end of the season, leading to rumours he could leave, but is now staying at Elland Road.
Kilgallon is set to play a more prominent role for the club in the First Division and he has put pen-to-paper on a two-year deal and is delighted to finally have his future sorted out.
"I am so pleased to have signed the new deal, Leeds mean so much to me," he said. "It is the club where I grew up, the club I have known all my life.
"The supporters have been superb and this gives me the chance to repay them for everything they have been through this season, and to try to get us back to where we belong.
"I know that the future here is much brighter than people are saying, we have a lot of good young players and I want to help the club regain it's pride."