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Guzman, captured on Saturday in Mexico with help from US agencies, had long run Mexico's infamous Sinaloa Cartel.
Robert Nardoza, a spokesman for the US Attorney's office in Brooklyn, said his office plans to seek Guzman's extradition to face a variety of charges.
The United States had placed a $5 million bounty on Guzman's head. Guzman's cartel has smuggled billions of dollars worth of cocaine, marijuana and methamphetamines into the United States, and fought vicious turf wars with other Mexican gangs.
He pioneered the use of sophisticated underground tunnels to smuggle drug shipments across the border and also became a major narcotics exporter to Europe and Asia in recent years.