One widespread misunderstanding is that polygraph interviews are for the purpose of determining if a person is trustworthy enough for a security clearance.  I believe polygraph examiners and agencies encourage applicants to believe this is the case as well.

But what they don't tell you is that the results of the polygraph examination may lead to a cancellation of an offer of employment based on 'suitability' considerations.  In these cases, which I believe are the majority, information is gleamed from the examination which is not disqualifying to a security clearance if it were formally adjudicated, but is frowned upon by the hiring agency.  When you are rejected based on these 'suitability' grounds you have much less recourse.  Further, when applying for a job at a different agency the 'derogatory' information may follow you even if that agency doesn't routinely use a polygraph!

This is the trap many find themselves in.  There are potential long term consequences to finding federal employment from taking a polygraph and being found 'unsuitable' even if you haven't engaged in any behavior which would render you unable to obtain a clearance.