The indictment in the US District Court for the Southern District of New York charges Hernández with cocaine importation conspiracy, possession of machine guns and destructive devices, and conspiracy to possess machine guns and destructive devices.
"As is charged in the indictment, Hernández abused his position as President of Honduras from 2014 through 2022 to operate the country as a narco-state," US Attorney General Merrick Garland said in April.
Hernández was extradited to the United States in April after he was arrested in February at the request of the US government.
About a month before his arrest, US federal prosecutors claimed Hernández helped an alleged drug trafficker deliver thousands of kilos of cocaine to the US in exchange for hefty bribes. His administration denied the allegation.
On Tuesday, Hernández entered the New York courtroom wearing a navy blue jail outfit and nodded toward those in attendance, including journalists and members of the public. On the way out several members of the public shouted at him, "murderer," "time to repent JOH," and "rat."
Hernández was listening via an interpreter. When asked how he would plea, he responded in Spanish "not guilty, your honor."
The former Honduran leader left office in January, having served eight years as president.
At the time of his extradition, the US Justice Department also unsealed an indictment alleging Hernández engaged in a conspiracy to protect and profit off smugglers moving cocaine from Central and South America into the United States.
Hernández's brother, Tony Hernández, is currently serving a life sentence in a US federal prison for drug trafficking.
According to court filings in that case, US authorities believe Hernández was a co-conspirator in the operation, funneling drug money to help fund his presidential campaigns. Hernández has repeatedly denied those allegations.
The next hearing for Hernández is scheduled to take place on September 28. Castel said he hopes to impanel a jury by early next year and set a tentative January 17, 2023 date for beginning of trial.