Guzman will appear Friday in a federal courtroom in Brooklyn, where he will stand trial at a later date. Stringent security measures were being put in place around the Manhattan jail where Guzman is to be held, a law enforcement source said. The Brooklyn Bridge will be closed while the drug lord is being transported to court.
The extradition may have been timed. Mexican authorities wanted to turn over Guzman, head of the Sinaloa cartel, before Friday's inauguration of President-elect Donald Trump, a US official told CNN. Trump angered Mexico during his campaign by demanding it pay for a border wall.
A Mexican deputy attorney general, however, said Trump's pending inauguration "had nothing to do with it."
"It was resolved today, and in terms of the international treaty, we had to immediately hand over the person requested by the United States," Alberto Elias Beltran said. "Not doing so would generate a nonfulfillment to the international norms, specifically with the treaty shared between Mexico and the United States."
Guzman, who was moved last year to Ciudad Juarez, was picked up by a team from the Drug Enforcement Administration, Immigration and Customs Enforcement and US marshals.
Six separate indictments across the United States lay out wide-ranging cases against Guzman and others, alleging they have brought in billions in drugs to the United States and laundered profits back to Mexico.
The extradition brings an end, at least for now, to Guzman's exploits in Mexico, which included a 2015 prison escape
through a mile-long tunnel that featured a motorcycle on tracks.
Guzman will not face death penalty in the US
A court in Mexico City on Thursday denied the drug lord's appeal of the extradition.
The US Justice Department thanked officials in Mexico "for their extensive cooperation and assistance in securing the extradition of Guzman ... to the United States."
Guzman and other cartel leaders were indicted in 2009 in US District Court in Brooklyn on charges of conspiring to import more than 264,000 pounds of cocaine into the United States between 1990 and 2005. The alleged traffickers are accused of sharing drug transportation routes and obtaining their drugs from Colombian drug organizations.
Guzman also faces charges in California, Texas, Illinois, Florida and New Hampshire. Mexico's foreign ministry has said it had received assurances that if convicted Guzman would not receive the death penalty. Mexico opposes death sentences.
Federal indictments described the Sinaloa cartel as an enterprise that uses murder, kidnappings and bribes.
The indictments refer to Guzman by various nicknames, including "El Rapido," "Papa," "El Viejo" and "El Chapo" (which means "Shorty." Guzman is 5 feet 6 inches tall.)
Over the years, Guzman gained near-mythic status in his home country. He has been the subject of ballads called "narcocorridos," a subgenre dedicated to cartels and their narco-violence.
Tunnels and a laundry cart getaway
For years, the notorious cartel leader proved slippery, staying just ahead of the law. He is known for using intricate tunnel systems for both evading authorities and moving the massive quantities of drugs that made the Sinaloa cartel so powerful.
Guzman's recapture in January 2016, after six months on the lam, represented a major success in what has been an embarrassing ordeal for Mexico. For many, "El Chapo" is a symbol of the Mexican government's corruption.
In 2001, he escaped from a prison in Jalisco in a laundry cart. Guzman was apprehended in February 2014 and escaped from Altiplano prison in July 2015 by crawling through an opening in the shower area of his cell block leading to a mile-long tunnel.
In August, Guzman's son was kidnapped from a Puerto Vallarta restaurant in what was perceived as an attempt to exploit the cartel's vulnerability. He was later freed.
'El Chapo' said drug trade would continue
The trafficking of heroin, marijuana, cocaine and methamphetamine into the United States from Mexico is an annual $19 billion to $20 billion industry, according to a Department of Homeland Security report.
And the Sinaloa cartel has traditionally held a dominant share of that market, thanks to Guzman's sophisticated business strategies and Sinaloa's control of trafficking routes.
A US Customs and Border Protection report that analyzed seizure data along the border between 2009 and 2010 found that "the removal of key personnel does not have a discernable impact on drug flows" into the United States.
Guzman seems aware that drug trafficking won't end once he's gone. "The day I don't exist, it's not going to decrease in any way at all," he told actor Sean Penn in an interview in October 2015.