Skilling, the top-ranking executive arrested so far in the scandal that shook Wall Street and Washington alike, was accused of participating in widespread schemes to mislead government regulators and investors about the company's earnings.
"I plead not guilty to all counts," Skilling told U.S. Magistrate Judge Frances Stacy, who set bond at $5 million. Skilling posted the bond with a cashier's check.
Former Enron employee Angie Lorio, who lost everything after 28 years at Enron, told CBS News Correspondent Lee Cowan she doesn't believe Skilling's claims that he was in the dark regarding company corruption.
"He had to have known what was going on, the guy is a scholar," Lorio said.
Prosecutors said Skilling, 50, faces up to 325 years in prison and more than $80 million in fines if convicted of all counts. Another court appearance to address trial scheduling is set for March 11.
The indictment names Skilling in 35 counts — 10 of them accusing him of insider trading that generated $62.6 million from stock sold from April 2000 through September 2001, about a month after he quit Houston-based Enron. According to the indictment, he sold shares in blocks ranging from 10,000 to 500,000 during that time, when Enron stock sold as high as $87 in September 2000 and as low as $31 in September 2001.
The indictment makes no mention of former Enron chairman Kenneth Lay, either by name or by title, but CBSNews.com Legal Analyst Andrew Cohen says it's just a matter of time.
"Skilling's surrender means that the investigation is almost to the top of the Enron pyramid, about as close to the top as you can get, with only Kenneth Lay himself now left to go after," said Cohen. "And I think we'll know soon whether Lay will be indicted because either Skilling will be able and willing to turn on his former boss or he won't."
Both Skilling and Lay, through their lawyers, have maintained their innocence of any wrongdoing related to Enron's failure.
"It would be a very difficult situation for Skilling to convince the jury that he was completely uninvolved," Howard Schilit, an accountant who specializes in detecting corporate corruption and accounting problems, told CBS Radio News. "The tone that's set in the organization is certainly set at the senior level."
Defense attorney Dan Petrocelli said prosecutors "were making a grave mistake" in pursuing Skilling "but they have decided to turn a blind eye."
"Jeff Skilling has nothing to hide," Petrocelli said. "He did not steal. He did not lie. He did not take anyone's money and in the 60 pages of charges filed by the United States government, they don't even accuse him of these things and it's not from lack of trying."
He said Skilling — unlike other former Enron executives who invoked their Fifth Amendment rights before Congress — had cooperated fully with investigators and government panels investigating the company's collapse.
"He has come forward, he has raised his right hand, he has answered the hard questions," Petrocelli said. "Jeff Skilling did nothing wrong. ... I guess they need a scapegoat. And I guess Jeff Skilling is their scapegoat."
Deputy Attorney General James Comey, who heads the Justice Department's corporate fraud task force, said Skilling and other executives were responsible for a "massive, complex scheme to give shareholders and the investing public the false appearance of financial strength and security at a time when Enron was, in fact, failing."
"The indictment of Enron's CEO shows that we will follow the evidence wherever it leads — even to the top of the corporate ladder," Assistant Attorney General Christopher Wray said.
Petrocelli said Skilling's legal team had given prosecutors results of a lie detector test Skilling took two years ago and passed "with flying colors." Comey declined to comment, except to note that sometimes defense lawyers "say the darndest things."
Skilling, flanked by a pair of attorneys, turned himself in at the Houston FBI offices just before daybreak. About 15 minutes later, his hands behind him in cuffs, he was placed in a car for the trip to the federal courthouse.
He becomes the highest-profile former Enron executive to date to face criminal charges and one of the most anticipated in the Justice Department's methodical investigation, which passed its two-year mark last month.
Two years ago, Skilling told two congressional panels that he knew nothing about serious problems at the energy trader before he quit after serving as CEO for six months. Skilling maintained that he believed Enron was financially healthy when he stepped down, citing personal reasons he has not explained.
The superseding indictment unsealed Thursday originally contained charges only against Richard Causey, Enron's former chief accounting officer. Causey, 44, was indicted a month ago and pleaded innocent. He is free on $500,000 bond.
Also mentioned by name in the indictment are former chief financial officer Andrew Fastow, who pleaded guilty and is cooperating with federal prosecutors, and former treasurer Ben Glisan, who pleaded guilty to conspiracy in September and became the first former Enron executive put behind bars.
Skilling's former boss, former Enron chairman Kenneth Lay, is referred to by title in the indictment twice: that Skilling reported directly to Enron's CEO and chairman; and that Enron's chairman/CEO mentioned a $1.2 billion writedown in shareholder equity during a conference call the day the company announced massive losses in October 2001.
Lay, who served as CEO before Skilling, has denied any wrongdoing related to Enron's failure though his lawyers.
The indictment said that from 1999 through late 2001, Skilling, Causey and their coconspirators "engaged in a wide-ranging scheme to deceive the investing public, the (Securities and Exchange Commission), credit rating agencies and others, about the true performance of Enron's businesses" by manipulating Enron's finances, making false and misleading public statements about Enron's financial performance.
The government was seeking to seize more than $50 million from Skilling's accounts, plus an 8,000-square-foot Houston mansion valued at $4.7 million.
Causey, who was fired in February 2002 after an internal probe concluded he failed to adequately look out for Enron's interests when the energy giant did deals with Fastow's partnerships, initially had been charged with six counts.
In the superseding indictment, he is charged with 31 counts, including two counts accusing him of insider trading. The document alleges he sold Enron shares generating $10.3 million from January 2000 to September 2000. The government is seeking forfeiture of Causey's suburban Houston home plus three accounts worth more than $3 million.
Both men are accused of wire fraud, securities fraud, securities fraud regarding presentations to securities analysts and of making false statements to auditors in annual representation letters and false statement to auditors.
Fastow pleaded guilty a month ago to two counts of conspiracy and agreed to help prosecutors pursue other cases. Fastow admitted that he and others manipulated Enron's books so the company would appear successful while using various partnerships to enrich himself, his family and chosen colleagues.
Fastow's lawyers said when he was indicted in October 2002 that he was hired to do off-the-books financing and that Enron's top brass approved and praised his work. Causey and Fastow reported directly to Skilling.