Guzman pleads not guilty, but the government has presented so much evidence - more than 300,000 pages and at least 117,000 recordings - that the defence complains they haven't had time to review it all. Guzman will join the ranks of mobsters John Gotti and Vincent Basciano, whose career-ending appearances in the Eastern District courthouse each brought in more than 1,000 potential jurors.
The judge ruled that just five news reporters, a fraction of the swarm of media representatives following the trial, will be allowed in the courtroom during jury selection.
Judge Cogan also raised concerns at the hearing about the prosecutors' planned case at the hearing.
The marathon Brooklyn federal trial, which is expected to last more than four months, will see Guzman face the United States justice system after twice escaping prison in Mexico, once hidden in a laundry cart and then slipping down a tunnel that reached his prison shower.
Guzman escaped prison twice in Mexico, once in a laundry basket in 2001 after running the cartel from a cell for seven years.
The now imprisoned brothers paid a steep price for flipping: Prosecutors say in 2009 their father was murdered in Mexico by a cartel hit team.
It is alleged that he spent a quarter of a century smuggling more than 155 tonnes of cocaine into the United States. Due to security concerns, the jurors' identity will be kept secret and they will be guarded by armed marshals on the way from court to home during the expected four-month trial.
Guzman's co-defendant Ismael "El Mayo" Zambada remains at large.
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Image: The shower where El Chapo escaped through a tunnel in 2015.
After Felix Gallardo was arrested in 1989, Guzman's Sinaloa cartel began its meteoric rise.
Some of the informants have already been absorbed into the United States witness protection programme and given new identities and homes around the country. Even Guzman's lawyers are in the dark as to all the former associates, hired hands or rivals who have turned informants.
That criminal pedigree has prompted authorities here to keep him in solitary confinement at a New York City jail.
The only visitors he is allowed are his lawyers and twin, seven-year-old daughters, from whom he is separated by thick glass.
Last year, there was a record 29,000 murders in Mexico. He was first apprehended by Mexican authorities in 2016.
He was arrested again by Mexican marines in February 2014 but escaped 14 months later before being re-captured in January 2016.
This time, Mexico made a decision to wash their hands of him and put him on a plane.