"The judges decided not to hear the (appeal for) protection" from extradition, the court source, who asked not to be named, told AFP.
Court dismisses Chapo extradition appeals
El Chapo's appeals to be extradited to the United States, have been declined by Mexico's supreme court.
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The source said the Supreme Court passed the appeals to a separate "collegiate" panel of judges for it to issue a ruling.
One of Guzman's lawyers, Andres Granados, said the defense team would study the court's arguments and may take the appeal to a regional human rights court.
The Sinaloa drug cartel boss was recaptured a year ago, six months after escaping from a maximum-security prison through a 1.5-kilometer (one-mile) tunnel that opened into his cell's shower.
He is facing two extradition bids, one in California for drug distribution and another in Texas on a slew of charges that include murder and money laundering.
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