The International Olympic Committee executive board notified Hamilton — a former teammate of Lance Armstrong — that he has been disqualified from his victory in the road race time trial at the Athens Games.
The medal will now go to Viatcheslav Ekimov, another former Armstrong teammate who already has two Olympic golds. American Bobby Julich will be moved up from bronze to silver, and Michael Rogers of Australia from fourth to bronze.
After years of denials, Hamilton told CBS's "60 Minutes" last year that he had repeatedly used performance-enhancing drugs. The IOC asked for documents from the U.S. Anti-Doping Agency before reallocating the medals.
"Hamilton will be asked to hand the medal back and there will be an exchange of medals with the other athletes," IOC spokesman Mark Adams said.
The IOC's move to change the medals was first reported Thursday by The Associated Press.
The IOC has an eight-year statute of limitations for changing Olympic results. The period expires at the end of this month.
USADA said at the time of Hamilton's doping admission that he had turned over his gold medal to the doping agency, but the IOC had not received it and the race result had not been officially overturned.
Hamilton sent a letter to IOC President Jacques Rogge on June 28 volunteering to give up the medal and withdraw his name from the record of Olympic champions.
"I very much appreciate that you have expressed regret for having used performance-enhancing drugs and that you hope that, through your example and future efforts, this will discourage others from using performance-enhancing drugs," Rogge replied in a July 16 letter to Hamilton.
The Russian Olympic Committee had repeatedly pressed for Ekimov to be upgraded to gold. The Russians failed in a 2006 appeal to the Court of Arbitration for Sport to have Hamilton's medal given to Ekimov.
The Russian will now receive his third gold, adding to his victories in the track team pursuit at the 1988 Seoul Games and the road time trial at the 2000 Sydney Olympics.
Ekimov rode with Armstrong on the U.S. Postal and Discovery Channel teams. He retired from cycling at the end of the 2006 season but remained in the sport as a director of the Discovery and RadioShack teams.
Before adjusting the results and reallocating the medals, the IOC wanted to be certain there was nothing in the U.S. investigation that implicated Ekimov and other riders or their coaches from the Athens cycling competition.
The IOC could have decided to disqualify Hamilton but not readjust the medals.
Hamilton had already come under investigation by the IOC during the Athens Games, when his initial doping sample indicated he had tested positive for a blood transfusion. The case was dropped after his backup "B'' sample was mistakenly frozen and couldn't be properly tested.
Hamilton tested positive a month later at the Spanish Vuelta. After serving a two-year suspension, he returned to cycling but tested positive again for a banned substance in 2009 and was banned for eight years.
Hamilton, who helped Armstrong win the Tour in 1999, 2000 and '01, accused Armstrong in the CBS interview of doping. Armstrong has denied using performance-enhancing drugs.
USADA officials brought charges of doping against Armstrong in June, threatening to strip him of his Tour de France victories from 1999-2005. A federal grand jury investigation of the cyclist ended four months earlier without indictments.
In a separate doping case, the IOC formally disqualified Italian race walker Alex Schwazer from the games on Friday after his positive test for EPO.
Schwazer, the 2008 gold medallist in the 50-kilometre walk, tested positive in a pre-competition test last month in Italy. He was expelled from the team by the Italian Olympic Committee.
"He has been disqualified and his accreditation taken away, but he has already sent home by the Italians," Adams said.
The IOC will also investigate Schwazer's coaches and entourage to see if they were involved in doping, and will consider retesting his samples from the Beijing Games.
"There is no hurry for that," Adams said. "We can wait."
The IOC stores doping samples from each Olympics for eight years to allow for retesting. Rashid Ramzi of Bahrain was stripped of his 1,500-meter gold medal after retests of Beijing samples showed use of CERA, an advanced version of EPO.
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