El Chapo will be appearing before a US court On Friday, January 20, on drugs, firearm and conspiracy charges.
His Sinaloa cartel is responsible for distributing hundreds of thousands of kilos of heroin, cocaine, methamphetamine and marijuana throughout the United States, reaping billions of dollars in profits, US prosecutors say.
Guzman was extradited from Mexico on Thursday, flown to Long Island and transferred by convoy to a jail in New York under heavy armed guard.
"Today marks a milestone in our pursuit of Chapo Guzman," Attorney Robert Capers told a news conference on Friday.
"Mr Guzman will be arraigned later today in the United States district court right here in Brooklyn on a 17-count sweeping indictment," Capers added.
The charges include leading and continuing criminal enterprise for alleged drug trafficking from late 1989 to September 2014, with multiple allegations that Guzman used corruption and violence to maintain control of his organization and conspired to murder rivals of the Sinaloa cartel.
He will be arraigned on 16 additional charges, including drug importation, illegal use of firearms and money laundering conspiracy "related to the billions of dollars" that his organization amassed, Capers said.
If convicted he faces life behind bars in an American prison. Prosecutors are also seeking to obtain a $14 billion criminal forfeiture order against him.
"Guzman's destructive and murderous rise as an international narcotics trafficker, is akin to that of a small cancerous tumor that metastasized and grew into a full blown scourge that for decades littered the streets of Mexico with the casualties of violent drug wars," Capers told reporters.
The same scourge made US cities such as Miami and New York "ground zero for that epidemic in the 1980s and 1990s," Capers said.