you can appeal. if you write an intelligent protest, did not admit to anything, there is a good chance you will get an appeal. I had 2 appeals. I failed all 3 tests but never used CMs. if you appeal and get another test, you would have a decision to make in that regard. if i had it to do over again, i woulda tried CMs on the final test. 
at the time i thought it to be wrong, but now my opinion is, if youre innocent, youre innocent and its just your pulse or finger sweat

Dear Martin,

The first step is one which you have taken, you sent them a letter strongly disagreeing with the findings.  If it was not certified return receipt, send one more so you can have something for your permanent records.  Write a quick memo about your whole polygraph process and individual exam proceedings and keep it with your records.

Be prepared to defend yourself two, five, or ten years from now against accusations that you "failed" the polygraph test given by the FBI.  Stress that it was a pre-screening test with no specific incident knowledge.  If they ask you how you know so much about specific incident test, tell them that after you were falsely accused, you tried to learn as much as you could in order to find out why you were falsely accused.

There are many agencies who do not use the polygraph but might question you on why you did not pass this one.

The polygraph as used in the FBI for employment screening has created many horror stories such as yours and it is a shame that our country's agencies have to feel that a candidate must be blacklisted in order to justify that they do not want them for employment.

I cannot understand why the FBI does not realize that they only hurt their long term chances of obtaining highly educated applicants like yourself with such treatment.  I doubt you will ever encourage anyone you know into applying for the FBI after your ordeal.

The labor pool of scientist is starting to dry up and this treatment is not helping.

Regards.

Martin,

As a result of your FBI application for employment, you now have a permanent FBI file branding you as a liar. It does not mean that you won't necessarily be able to obtain a security clearance (with an agency other than the FBI), but it is a black mark that will make it more difficult.

Hi Opp, thanks for the kind words.

I did not prepare for the polygraph at all. No counter measures. Througout the course of the test I was extremely nervous, and when, after the first round, the examiner told me that I was borderline on some questions, I began to feel this nervousness ramp up. Both my heart and breathing rates were all over the place (the examiner told me to breath naturally numerous times). With each additional round, I knew that something was up, and this fed into the nervousness. When he began to verbally push by saying "Be 100%!" during the actual questioning, I felt extremely wound up. 

A little background- I am a PhD researcher with history of anxiety. Never medicated for it, and beat it on my own. However, I always seem to exist in a mild state of neurosis. I don't think this would have affected my ability to be an agent, and on contrary, I have found that a heightened sense of awareness is quite beneficial to my attention to detail, curiosity, and creativity. During the test I felt like I was relapsing! 

Marti,

I am sorry to hear about your experience. One of the things that has me with a great deal of anxiety is the fact that I have invested so much time an energy in the application process and in the end the probabilities are that I may fail. I am sure guys like George and others can further assist you in explaining to you the consequences of failure. From what I understand they are not good. These are the chances we take when we try to accomplish our dream job. Let me ask you – how well did you prepare for the test, and were you nervous from the beginning?

Opp

Hi,

So I did fail the SA-polygraph about a year ago. I was really disappointed as one might imagine, having dedicated much effort to the application process- the fitness test, panel interview, etc.

I was nervous about the question regarding the number of times I had smoked marijuana, because I could remember close to 15 instances, but was playing mental games wondering if I had left out some instances. Funny thing was that I didn't have any problems with that question, but got nailed on something about selling drugs. Furthermore I thought the tester was an ass, because he kept telling me that I was borderline on some questions and I think he became frustrated by the fact that it was fairly indeterminate- so much so, that on the last round, he actually yelled at me during a question "c'mon, give 100%!" That move really stressed me out, and I bet that pushed me right into the lying zone on the machine.

Okay, fine. I know the truth, but they do not. They also missed out on someone who would have really contributed to the bureau. I'm over the job now, although I still get these pangs of disappointment from time to time when I fell helpless about terrorism.

My question is, what now? I sent them a letter strongly disagreeing with the findings. I'm guessing that I can never obtain security clearance for anything? Am I on some sort of blacklist for certain jobs? What does this mean for me for the rest of my life?

Opinions, information would be greatly appreciated.

Thanks,
Martin