The conviction carries a mandatory life sentence. El Chapo was once one of the richest, most powerful and feared men in the world. Tuesday he could only muster a blank stare as the jury found him guilty on all 10 federal counts.
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"Today's verdict is justice for the men thousands upon thousands of victims of overdose," said Ray Donovan, New York DEA special agent in charge.
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In addition to New York, Guzman was charged in five other states, including Illinois. Authorities had hoped to try him in Chicago but that seems unlikely now. However, the work of authorities in Chicago played an important role in the New York case, including providing star witnesses.
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Hailing from Little Village, the Flores twins were precocious and prolific, learning the cocaine trade at age seven. By 17 they were overseeing the Chicago franchise of El Chapo's criminal operation.
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But a decade ago the brothers flipped, and their cooperation with the government helped take down one of history's most notorious criminals.
"Guzman's deadly drugs destroyed many American families for nothing more than greed and power," said DEA Acting Administrator Uttam Dhillon.
Among the more than 50 witnesses called was Pedro Flores, one of the twins. He testified he and his brother imported 38 tons of cocaine from El Chapo, sending $800 million in cash from Chicago to the Sinaloa cartel.
Flores even wore a wire for the feds, recording conversations with cartel associates and even Guzman himself.
"This was an extraordinarily strong case with the strongest sorts of evidence that you can imagine, like wiretaps and others," said ABC7 legal analyst Gil Soffer.
The Flores twins pleaded guilty in their own Chicago case and are currently serving 14-year sentences. Once out of prison, they will likely spend the rest of their lives in witness protection.
El Chapo trial: Drug cartel kingpin found guilty, Chicago trial unlikely
During the nearly three month long trial Guzman, 61, was painted by prosecutors as a murderous thug who wielded violence and fear as the longtime head of the Sinaloa cartel, in charge of trafficking hundreds of thousands of pounds of drugs, money laundering, and conspiring to murder several of his rivals.
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"This conviction we expect will bring a sentence of life without the possibility of parole. It is a sentence from which there is no escape and no return," said Richard Donohue, U.S. Attorney for the Eastern District of New York.
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Prosecutors called more than 50 witnesses, but the defense argued El Chapo was a scapegoat, set up to take the fall by the cooperating witnesses.
"We fought like hell, we fought like complete savages, and left it all on the battlefield for Joaquin Guzman," said Jeffery Lichtman, defense attorney.
Authorities said the verdict was a message to other traffickers.
"We're going to grind away. We're not gonna stop. We're going to find them, we're going to indict them. We're going to extradite them," said Brian McKnight, DEA special agent in charge for Chicago.
Click here for complete ABC7Chicago coverage of Joaquin "El Chapo" Guzman