Sorry to hear your story.  Which agency did you apply to?  Was it CIA?

I am a CIA reject.  I got the Conditional Offer of Employment (COE) and then "failed" my polygraph during my 3-day processing at the CIA Dulles Discovery Building (13900 Air & Space Museum Parkway, Chantilly, VA).  I got a certified letter a couple of months later saying I had been "denied access to classified information" and my COE rescinded.   I had a security clearance, have never been arrested, no criminal record, no drug issues, no foreign contacts, no security violations.  Yet, I'm some sort of security risk?

I went ahead a filed a Freedom of Information Act / Privacy Act (FOIA/PA) request, which came through with a copy of my background file.   There wasn't much there since the CIA didn't run my background check yet for my clearance.  All I really got was a copy of my SF-86 security clearance form and a completely censored copy of my polygraph report (the report was essentially blank pages with my name and occupation on the header, the polygraph info was redacted).  I requested a "review of the decision", hence an appeal, and it took 2 years before I heard anything.  My appeal was denied.  I was granted one final appeal which was also denied.  No surprise.  I have never heard of any applicant for the CIA successfully appealing their negative polygraph result.  It screwed my cleared career for a while but I eventually got hired by another agency and got my TS/SCI clearance, no polygraph needed in this case.   

The polygraph is garbage and they accuse EVERYBODY of something, usually crime or drugs or foreign contacts, to see if you'll confess to something they never would have found out about in the first place.  They have to reject a certain number of applicants to prove that the polygraph "works", which is doesn't.  You just drew a bad straw.  As did I.  Sucks for both of us.  I compare polygraphers to psychics, mere hogwash.

I would suggest you file a FOIA and appeal the decision, as I did, but don't expect anything.  Forget about it, and move on.  The appeal doesn't cost anything and at least you'll have on record that you did appeal and completely disagree with their decision.  That is the only advantage of appealing.  You can still have another good cleared career without these polygraph-agencies.  As for re-applying, I don't know.  I haven't found any stories online about people getting hired by the same agency that rejected them previously due to a failed poly, but I'm sure it does happen.

While I haven't personally applied for CIA employment, I concur with what "a cia reject" wrote. I'm not aware of a single case where an applicant for federal employment was later hired by an agency whose polygraph he or she "failed." That doesn't necessarily mean that there aren't any such cases, but if there are, it would seem that they are exceedingly rare.

Thank you George, I hope for the best. 

@"a cia reject" 

During the polygraph, I was accused of committing a "major" crime. I said, I tried hacking into the hackers group Anonymous the day before they took down the FBI website. They wanted to know my process, how it went about doing it. After telling them how and i also mention I did this with good intentions, for the greater good, that if i can locate and identified 1 of them, It could really give me a boost in my academic career.

My letter stated, I'm a member of Anonymous.

KC1 wrote on Oct 24^th, 2013 at 10:33am:

Once a polygrapher accuses you of lying, he goes into a frozen-mind mode where he can hear only words that confirm the accusation.  All other information is filtered out.

Your mistake seems to be that you responded to his accusation with actual information.  Unfortunately your response included the words "hackers group Anonymous", "I tried hacking" and "took down the FBI website", with maybe "boost in my academic career" as a condiment.  Nothing else made it through his filter.

Never tell a polygrapher anything.  Polygraph sessions are unmonitored and unrecorded (they won't even let you have the chart), so when the Polygrapher lies about what you said, you have no evidence to counter him.

Giving him a hook to hang his lies on encourages him to think that you can be bullied.  It boosts his confidence and erodes yours, so that you don't even want to write the letter disputing his findings.

Thank you George.  I stand corrected.  Now I wonder if the policy of not recording poly sessions is as widespread as I thought.

Thanks guys, I really got the bad hand here. it's such a shame the way how things are done. 

Should I write and ask at the same time to send my investigation file and to review my case? 

Or only do one? and which one.

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How does one appeal their CIA security clearance denial?  Is that done through the same office that handles the FOIA/PA requests?