The jury in Guzman's three-month trial will begin its deliberations on Monday. Jurors will be asked to begin deciding the verdict for Guzman, who faces life in prison if convicted. A federal judge in Brooklyn first gave hours-long instructions to jurors, and reminded them of the oath they took to proceed "without fear or favor".
The 11-week trial, which featured testimony from more than 50 witnesses, offered the public an unprecedented look into the inner workings of the cartel, named for the state in northwest Mexico where Guzman was born in a poor mountain village.
A key government co-operator, Colombian drug trafficker Alex Cifuentes, claims in the documents that Guzman directed him to put "powdery substances" in the drinks of girls as young as 13.
She said El Chapo - "The Shorty" in Spanish, for his diminutive stature - wanted to escape again "because he is guilty and he never wanted to be in a position where he would have to answer for his crimes". "He wanted to avoid sitting right there".
In his closing, lawyer Jeffrey Lichtman assailed the case as a "fantasy" and urged the jury not to believe witnesses who "lie, steal, cheat, deal drugs and kill people" for a living.
Cifuentes used this service himself three or four times, having sex with girls as young as 15-years-old, the government said in the documents, adding he "witnessed the defendant do the same on multiple occasions, with girls as young as 13 years old".
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The papers were unsealed late Friday at the request of The New York Times and Vice News.
The allegations come as a jury is about to start deliberating in his U.S. drug-trafficking case.
Eduardo Balarezo, one of Guzman's attorneys, said his client denies the "extremely salacious" allegations that "lack any corroboration and were deemed too prejudicial and unreliable to be admitted at trial". DEA agent Victor Vazquez told jurors he would only work with the Mexican marines when trying to capture Guzman and other leaders of the Sinaloa cartel, because that wing of the armed forced were viewed as less susceptible to corruption.
Nearly all of them had heard of Guzman before the trial began, but said they could be impartial. He twice escaped from prison in Mexico, and will face the possibility of life in a USA prison if convicted.
El Chapo's wife, Emma Coronel Aispuro, departed court on Monday as jurors continued deliberations without reaching a verdict in the trial.