Many of the plaintiffs in the Puerto trial, including Spain's anti-doping agency and the World Anti-Doping Agency want Santamaria to release the bags to investigators for further testing after the Puerto trial concludes.
The trial is limited to doping in cycling, even though athletes in other sports were also reportedly implicated in blood doping with Fuentes. Such evidence could be contained in the bags.
In the Puerto trial, Santamaria can rule only on matters covered by Spanish law as it applied in May 2006, when doping in sport was not illegal.
As the hearing ended, Hamilton apologized to Santamaria for cheating.
"My biggest fear was that something like this (trial) would happen," he told the judge.