Skilling, 50, appeared before a federal magistrate after surrendering earlier in the day to FBI agents and being led off in handcuffs for the court appearance.
Skilling is charged in a 42-count indictment returned Wednesday by a federal grand jury in Houston. He allegedly conspired to artificially pump up Enron earnings for his own personal gain.
Between 1998 and 2001, Skilling received $200 million from the sale of inflated Enron stock, clearing an $89 million profit on top of his $14 million salary, the indictment states.
Daniel Petrocelli, one of Skilling's attorneys, told reporters his client has passed a polygraph test and that the government has no case against him.
"He passed with flying colors, with no hesitation, and the government know's it," he said. "They know they don't have a case against this man. "
Skilling is the highest-ranking former Enron executive charged in the federal investigation into the collapse of the Houston energy giant that cost shareholders millions of dollars and laid-off workers their retirement savings.
Enron Chairman Ken Lay is still under investigation but he has not been charged.
Former Chief Financial Officer Andrew Fastow pleaded guilty Jan. 15 and agreed to a 10-year prison for two counts of conspiracy. Fastow, who worked closely with Skilling, is expected to cooperate in the investigation.