Joaquín Guzman Lopez made his first brief court appearance at the Dirksen Federal Building.
He pleaded not guilty Tuesday in front of Judge Sharon Johnson Coleman.
The 38-year-old appeared wearing an orange jumpsuit.
Assistant U.S. Attorney Andrew Erskine went through the five trafficking, conspiracy and money laundering charges. For one of the charges, the maximum sentence is death because the arrests took place on American soil.
Accused cartel leaders arrested in Mexico would have faced extradition, and the terms of a US-Mexico treaty that prohibits extradition in a death penalty case.
Jeffrey Lichtman is representing Guzman Lopez, who is one of four sons of Joaquin Guzman, commonly known as "El Chapo."
The four sons are known as the "Chapitos," but the benign nickname can't soften the edges of what authorities say they do: sell drugs that take thousands of American lives. They also kill those who get in the way of their illicit business, according to the numerous indictments that stand in Chicago and elsewhere.
El Chapo was once the leader of the Sinaloa cartel, and considered one of the most powerful drug traffickers in the world.
READ MORE: A son of El Chapo helped capture Sinaloa cartel leaders, officials say
El Chapo's son surrendered to U.S. authorities in El Paso, Texas last Thursday, which led to the arrest of Ismael Zambada, who goes by "El Mayo."
The 76-year-old El Mayo was allegedly left to oversee the cartel after El Chapo was convicted and sentenced to life in prison.
El Mayo allegedly co-founded the Sinaloa cartel with El Chapo, which supplied 80% of Chicago's fentanyl, cocaine, heroin and methamphetamines over the decades.
ABC7 Chicago legal analyst Gil Soffer called this a huge case for federal prosecutors.
"It's a very big case," Soffer said. "It's a big win for DOJ to be able to get the leaders of this cartel. They've been looking to get them for years and years, and what makes it all the more interesting is how he got here: the intrigue, the betrayal, the back-stabbing, the sons who turned against their fathers. You'd have to look long and far to find a story this complex and interesting, but this is a serious get for the DOJ."
Zambada and Guzman Lopez are accused of leading the cartel's criminal operations, including its deadly fentanyl manufacturing and trafficking networks.
Federal authorities say Guzman Lopez actually assisted with Zambada's capture. And rumors are swirling about whether that alleged cooperation was for a better plea deal.
It's not clear why Guzman Lopez flew on a private prop jet from Mexico to an area near El Paso, Texas with Zambada.
"It seems that there was some plan in advance hatched by Guzman, certainly," Soffer said. "If the goal of Guzman and his henchmen was to eliminate El Mayo, then you think they could simply have killed him. The fact that they went through the effort of bringing him here to be prosecuted would suggest that Guzman has arranged for, or is hoping for some sort of lenient treatment by the U.S. authorities."
El Mayo's attorney and government officials claim Guzman Lopez violently forced Zambada to the U.S.
"So his lawyer is certainly going to argue that it matters. He will argue that he was forcibly abducted and that violates his due process rights. But that's probably a losing argument. What matters is what happens once he's on U.S. soil, and if he was treated appropriately here. Then, this prosecution can probably go forward," Soffer said.
Zambada was one of the Drug Enforcement Administration's most wanted fugitives.
The U.S. had been offering a $15 million reward to track him down.
Zambada entered a not guilty plea to all charges in El Paso on Friday.
Lichtman said Tuesday his client did not kidnap El Mayo, and has not made a deal with the government.
"I'm not sure exactly what, what actually happened, but all I know is that walking in, Guzman is in Chicago, and I'm representing him," Lichtman said. "We've got no agreement with the government. There has never been an agreement with the government, with Joaquin Guzman Lopez. There is no agreement, period. That's, if you like, for there to be an agreement. I don't know how this case is going to resolve. It's not always up to me. I have to look at the evidence. I, you know, reviewed the evidence as to how it reflected on his brother, Ovidio."
He went on to say, "It's very interesting. I don't disagree on the allegations, but, as I said, the allegations keep changing by the day. I'm sure that eventually everything will come out. I just don't want to feed the beast."
Guzman Lopez is next due in court Sept. 30, and remains in custody.