Jury selection is expected to take a few days with opening statements set to start on November 13.
He said he was concerned that the prosecutors had indicated that they were prepared to present evidence that Guzman was involved in more than 30 murder conspiracies, even though the charges against him are for drug trafficking.
Security around Guzman has also been tight ahead of the trial.
During the trial, jurors will reportedly be accompanied by US Marshals to and from the courthouse, and their names and addresses will be kept secret. US authorities have described the group as one of the most powerful drug trafficking organizations in the world.
Prosecutors say Joaquin Archivaldo Guzman Loera led the Sinaloa Cartel, an alleged criminal enterprise that imported and distributed massive amounts of drugs into the United States, between January 1989 and December 2014.
For pretrial hearings, authorities transported the accused Mexican drug lord to and from the federal jail in lower Manhattan by shutting down the Brooklyn Bridge to make way for the police motorcade.More news: Amazon plans to split HQ2 evenly between two cities
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Image: The shower where El Chapo escaped through a tunnel in 2015. Prosecutors say the Sinaloa Cartel, named for Guzman's home state, smuggled more than 200 tons of cocaine into the United States.
Arrested for the first time in Guatemala in 1993, El Chapo spent more than seven years in a Mexican prison before his first escape in 2001. The dramatic escape triggered a worldwide manhunt that ended six months later in a deadly shootout in Los Mochis, a coastal city in Sinaloa.
That tipped off investigators to his location. Others recalled how he did an interview with actor Sean Penn while he was on the run. He was recaptured in Mexico in February 2014.
"Guzman Loera is accused of using violence, including torture and murder, to maintain an iron-fisted grip on the drug trade across the U.S. -Mexico border, ' then-Brooklyn U.S. Attorney Robert Capers said". The mammoth trial in a Brooklyn federal court, which will cost millions of dollars and is expected to last more than four months, will see Chapo, one of the world's most notorious criminals, face the U.S. justice system. In the United States, opioid addiction has spiralled into an epidemic. "Guzman Loera made billions of illicit dollars".
A Mexican official told Reuters at the time that the move was a show of goodwill to incoming US President Donald Trump, who was inaugurated the next day, though Alberto Elias Beltran, Mexico's assistant attorney general for global affairs, denied any connection. McCoy reported from NY.