According to the indictment, Guzman is responsible for ordering thousands of murders during the years his Sinaloa Cartel funneled 200 metric tons of cocaine as well as other drugs into the United States, pulling in $14 billion (€12.3 billion).
Potential jurors, including a Michael Jackson impersonator, arrived to court to see it surrounded by heavily armed guards and bomb sniffing dogs that had staged a perimeter.
Most of the jurors questioned at the outset said Guzman's name "sounded familiar" to them. If convicted, he faces life in prison.
He was recruited by Guadalajara cartel boss Miguel Angel Felix Gallardo, known as "The Godfather" of Mexico's modern drug cartels. The 12 jurors and six alternate jurors chosen will be escorted to and from the courthouse by armed USA marshals.
A look at those concerns for a trial that is starting Monday with jury selection.
Opening statements are tentatively scheduled for November 13.
One of Mexico's most notorious drug lords will go on trial in the U.S. later on Monday.
After two massive prison breaks by El Chapo in Mexico, authorities in the United States are taking every precaution to keep their notorious prisoner behind bars.
A moment of levity came when one potential juror was asked about a deli near his workplace stocking a sandwich called "El Chapo". Both were dismissed. One said she "read (Guzman's) family will come after jurors and their families" and the other said she was concerned about safety "in general". The Sinaloa cartel that Guzman founded in 1989 is still hugely powerful. He twice escaped from maximum security prisons in Mexico, and authorities have sought to protect trial witnesses from possible cartel retribution.
The jury will determine whether Guzman - the father of two whose nickname means "shorty" as he is only 5ft 2ins tall - is guilty or not of 11 trafficking, firearms and money laundering charges.
Prosecutors describe Guzman as one of the most unsafe and feared drug kingpins, who between 1989 and 2014 ran the world's largest drug trafficking organization. In the United States, opioid addiction has spiraled into an epidemic. U.S. prosecutors contend that from 1989 to 2014, the cartel smuggled at least 340,892 pounds (154,626 kilograms) of cocaine into the United States, as well as heroin, methamphetamine, and marijuana, raking in $14 billion.
But that could create a logistical nightmare during the trial, and there is speculation that "El Chapo" is being held in a cell deep within the Brooklyn courthouse.
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