The dirty little secret behind the polygraph is that the "test" depends on trickery, not science. The person being "tested" is not supposed to know that while the polygraph operator declares that all questions must be answered truthfully, warning that the slightest hint of deception will be detected, he secretly assumes that denials in response to certain questions -- called "control" questions -- will be less than truthful. An example of a commonly used control question is, "Did you ever lie to get out of trouble?" The polygrapher steers the examinee into a denial by warning, for example, that anyone who would do so is the same kind of person who would commit the kind of behavior that is under investigation and then lie about it. But secretly, it is assumed that everyone has lied to get out of trouble.
The polygraph pens don't do a special dance when a person lies. The polygrapher scores the test by comparing physiological responses (breathing, blood pressure, heart, and perspiration rates) to these probable-lie control questions with reactions to relevant questions such as, "Did you ever commit an act of espionage against the United States?" (commonly asked in security screening). If the former reactions are greater, the examinee passes; if the latter are greater, he fails. If responses to both "control" and relevant questions are about the same, the result is deemed inconclusive.
The test also includes irrelevant questions such as, "Are the lights on in this room?" The polygrapher falsely explains that such questions provide a "baseline for truth," because the true answer is obvious. But in reality, they are not scored at all! They merely serve as buffers between pairs of relevant and "control" questions.
The simplistic methodology used in polygraph testing has no grounding in the scientific method: it is no more scientific than astrology or tarot cards. Government agencies value it because people who don't realize it's a fraud sometimes make damaging admissions. But as a result of reliance on this voodoo science, the truthful are often falsely branded as liars while the deceptive pass through.
Perversely, the "test" is inherently biased against the truthful, because the more honestly one answers the "control" questions, and as a consequence feels less stress when answering them, the more likely one is to fail. Conversely, liars can beat the test by covertly augmenting their physiological reactions to the "control" questions. This can be done, for example, by doing mental arithmetic, thinking exciting thoughts, altering one's breathing pattern, or simply biting the side of the tongue. Truthful persons can also use these techniques to protect themselves against the risk of a false positive outcome. Although polygraphers frequently claim they can detect such countermeasures, no polygrapher has ever demonstrated any ability to do so, and peer-reviewed research suggests that they can't.
Lie detectors don't work - and that is the truth!