Mr Heroy estimates the trial will cost U.S. taxpayers "more than US$50 million", a price tag that includes protection programmes for at least some of the hundreds of witnesses expected to testify.
Years have been spent piecing together evidence against Guzman, 61, who was extradited from Mexico in 2017 after twice escaping prison - first hidden in a laundry cart, then slipping down a tunnel that reached his prison shower.
Arrested for the first time in Guatemala in 1993, Guzman spent more than seven years in a Mexican prison before his first escape in 2001. There are extra precautions being taken for witnesses and jurors to ensure their safety, as well.
A look at those concerns for a trial that is starting Monday with jury selection. 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.
An anonymous pool of potential jurors - gleaned from 1,000 New Yorkers who were sent a 31-page questionnaire - will arrive in Brooklyn federal court, where they will lay eyes on the runty drug baron himself as they are probed as potential panelists at Guzman Loera's trial on drug-conspiracy charges.
Guzman, who allegedly continued to run the world's largest drug-trafficking operation even while behind bars in Mexico, now faces the possibility of life imprisonment in the United States. The U.S. Drug Enforcement Administration says he was able to remain a force by communicating with his son and other cartel leaders through lawyers and others who visited him at the Altiplano prison outside Mexico City.
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US District Judge Brian Cogan, prosecutors and defence lawyers on Monday morning questioned 20 potential jurors, and have so far ruled out five. Jurors will also be escorted by United States marshals to court daily while remaining anonymous throughout the trial.
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.
Guzman was extradited to the United States in January 2017 on an indictment that detailed his alleged reign over a merciless trafficking organization controlled through murder and torture. Some are expected to testify under aliases.
Mexican authorities captured Guzman and an associate in January 2016 fleeing a raid on a house where he had been staying in northwest Mexico.