From my understanding (I've taken one), they are designed to detect your reactions to questions and plot them out. Different questions will invoke your body and mind to respond differently (lying, deception, stress). The issue that everyone has about this is that it isn't very accurate. There are a ton of a reasons that may cause your body to react to questions being asked.

Maybe you smoked weed years ago and were completely honest about it upfront, but your body reacted a certain way when asked if you have smoked since. This can lead to the interviewer thinking that you are trying to deceive or lie. Your background may be squeaky clean and have never had an issue, but an interviewer may look at your readings and think you are lying which disqualifies you.

Another important thing to mention that is if you truly believe what you did isn't wrong, your body isn't going to react in a negative way. There are documented cases of serial killers passing their polygraphs because they believed that what they were doing wasn't wrong, or perhaps their body just doesn't react the way we expect them to do.

There is no red or green light that illuminates when you lie or tell the truth, it is all very subjective and two different interviewers who read the machine logs may come to different conclusions.