- February 2000 - Mariano Faget, a naturalized citizen working for the Immigration and Naturalization Service was arrested for passing classified information to Cuba. He was sentenced in 2001 to 5 years in prison for disclosing classified information and other related charges.
- April 2000 - Timothy Steven Smith was charged with espionage after being caught stealing disks and five Confidential documents from a ship in the Pacific Fleet. He pled guilty to stealing government property and assaulting an officer and was convicted to 260 days in prison, including time served.
- June 2000 - George Trofimoff, a naturalized citizen of Russian parents, was arrested for spying for the Soviet Union and Russia since about 1969. Having retired as a colonel in the United States Army Reserve, he was the highest-ranking military officer ever accused of spying. He was convicted and sentenced to life imprisonment.
- February 2001 - Robert Philip Hanssen was arrested for spying for the Soviet Union and Russia for most of his 27 years with the Federal Bureau of Investigation. He passed thousands of pages of classified documents on nuclear war defenses and Sensitive Compartmented Information and exposed three Russian agents of the United States, two of whom were tried and executed. He pleaded guilty to espionage and was sentenced to life in prison.
- August 2001 - Brian Patrick Regan, a contractor for TRW working at the National Reconnaissance Office was arrested for attempting to sell Top Secret Sensitive Compartmented Information to foreign governments. He was convicted of attempting to sell classified information to Iraq and China and was sentenced to life in prison without parole.
- September 2001 - Ana Belen Montes, a senior intelligence analyst with the Defense Intelligence Agency passed classified military and intelligence information to Cuba for at least 16 years. She pleaded guilty and was sentenced to 25 years in prison and 5 years of probation.
- 2002 - The Department of Justice Inspector General reported that 212 functional weapons, 142 inoperable training weapons, and 317 laptop computers were lost, missing, or stolen during a 28-month review period.
- March 2003 - 18 year-old Adil Yahya Zakaria Shakour breached network security at Sandia National Laboratories and defaced an Eglin Air Force Base web site. Shakour is a Pakistani citizen living in the United States. He pleaded guilty to computer and credit card fraud charges.
- April 2003 - A security officer at Lawrence Livermore National Laboratory loses an electronic access badge. The loss is reported to an immediate supervisor, but senior Livermore managers are not notified until late May, at which point the badge was deactivated.
- April 2003 - Security officers at Lawrence Livermore National Laboratory discover that a set of keys to the gates of the laboratory are missing. Locks are changed.
- February 2004 - Ryan Gilbert Anderson, a member of the Washington National Guard was charged with 5 counts of attempting to provide aid and information to Al Qaeda. A court martial sentenced him to life in prison.
- 16 July 2004 - Sandia National Laboratories announced that they had located a classified floppy disk that had been discovered missing on June 30 during a routine inventory. It was missing because it was improperly transferred to a different organization at the lab.
- October 2006 - A drug-related investigation at a private residence found classified documents and a thumb drive containing classified information, all from Los Alamos National Laboratory, at the home of Jessica Quintana, a former subcontractor to the laboratory.
- December 2006 - Petty Officer Ariel Weinmann of the United States Navy pleaded guilty to espionage, desertion and other charges. His case is notable as an espionage case where the Navy and trial court officials have denied access to basic information, including the court docket.
- February 2007 - The Department of Justice Inspector General reported that "over a 44-month period the FBI reported 160 weapons and 160 laptop computers as lost or stolen."
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