DoD uses a directed-lie "control" question "test" known as the Test for Espionage, Sabotage, and Terrorism  (the latter word having been recently added).  You'll find it described in my article, "The Lying Game: National Security and the Test for Espionage and Sabotage."

Unlike the FBI pre-employment polygraph, it seems that almost everyone ultimately passes the DoD polygraph, and that the only way to "fail" is to make a "substantive admission." See the message thread, How to Pass the DoD CI-Scope Polygraph.

For more on other types of polygraph examinations, including the probable-lie "control" question "test" used by agencies like the FBI, as well as information on how to reduce the risk of becoming a false positive, see The Lie Behind the Lie Detector.