Mexico extradited drug kingpin Joaquin El Chapo Guzman to the United States after his final appeals were rejected -handing US authorities a massive drug case on the eve of Donald Trump's inauguration.

Guzman is the head of the Sinaloa cartel, which is accused of generating much of the deadly violence in Mexico and providing tons of drugs to the United States was extradited yesterday, and had twice escaped from prison.

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He had been fighting his extradition ever since he was recaptured almost exactly a year ago in his home state of Sinaloa, following his second daring jailbreak.

The Mexican government "delivered Mr Guzman Loera to the authorities of the United States" after the Supreme Court and a court of appeals rejected his latest bids to avoid extradition, the foreign ministry said in a statement.

The appeals court ruled that the extradition conformed with a bilateral treaty and that Guzman's rights had not been violated, the statement said.

The government did not say to which state Guzman was sent. CNN and ABC News reported that Guzman was headed to New York.

A US government official, who spoke on condition of anonymity, would only confirm to AFP that Guzman was already on US soil.

The US Department of Justice confirmed the extradition in a brief statement, only saying that information about his initial court appearance would be "forthcoming," without saying where he would be held.

"The Justice Department extends its gratitude to the government of Mexico for their extensive cooperation and assistance in securing the extradition of Guzman," it said, adding that he had been charged in six separate indictments.

In May, the Mexican foreign ministry approved extradition bids from California, where he is wanted for drug distribution, and Texas, where he faces a slew of charges including murder and money laundering.

Trump, who takes office today, has publicly clashed with Mexico over trade and immigration issues. The Republican president-in-waiting has pledged to build a wall on the US-Mexican border.

Guzman's extradition caps a Hollywood-worthy cat-and-mouse game between Mexican authorities and the slippery drug lord, who escaped twice from prison.

He was first captured in Guatemala in 1993, only to escape from a maximum-security prison in western Mexico in 2001 by hiding in a laundry cart.

Marines backed by the US Drug Enforcement Administration arrested him in February 2014 in the Sinaloa resort of Mazatlan, where he was staying with his wife and twin daughters.

President Enrique Pena Nieto refused to extradite Guzman at the time, insisting that he would face justice at home.

But Guzman escaped from prison again in spectacular fashion just 17 months later.