Federal Judge Edward Nottingham also ordered Nacchio to pay a $19 million fine and forfeit $52 million he gained in illegal stock sales. As of October 15, 2007 he was free on bail, appealing his conviction on the basis that the U.S. government retaliated against Qwest for his refusal to give customer data to the National Security Agency. On March 17, 2008, the U.S. Court of Appeals for the Tenth Circuit overturned his conviction on the basis of defense expert witness testimony that was improperly excluded, and ordered a new trial before a different trial judge. On February 25, 2009, Nacchio lost his appeal in a 5-4 ruling by the 10th U.S. Court of Appeals. He was ordered to immediately begin serving his six-year prison sentence. His defense team will now attempt to petition the United States Supreme Court. Nachio reported to the Federal Prison in Schuylkill County, Pennsylvania on April 14, 2009 to serve his sentence.
On March 15, 2005, Nacchio and six other former Qwest executives were sued by the U.S. Securities and Exchange Commission. They were accused of a "massive" $3 billion financial fraud between 1999 and 2002 and of benefiting from an inflated stock price.
In its case, the government stated that Nacchio continued to tell Wall Street that Qwest would be able to achieve aggressive revenue targets long after he knew that they could not be achieved. This helped it buy up regional phone rival US West, the government alleges. For his part, Nacchio maintained that he believed Qwest would soon be receiving several large government contracts. On November 21, 2005, The Wall Street Journal reported that Nacchio "believed Qwest was doing well because it was getting lucrative secret national-security-related work from the federal government." Nacchio claimed that he was not in a rightful state of mind when he sold his shares because of problems with his son, and the imminent announcement of a number of government contracts.
Nacchio was indicted on December 20, 2005 on insider trading charges in Denver, Colorado. He was forced to surrender his passport for fear that he would flee the country. The indictment against Nacchio charged him with 42 counts of insider trading. Each count carries a potential 10-year jail term and corresponds to a sale of Qwest shares, including a flurry in April-May 2001, when Nacchio sold almost $39 million in stock. At the time, Qwest was trading between $41.12 and $38.31.