As Dr. Alan Zelicoff, M.D. has pointed out, "there are no guidelines, textbook chapters, or review articles in any medical, psychology or psychiatry journal that describe medical contra-indications to the polygraph."

To answer your questions:

1) Polygraphers will happily polygraph just about anyone with an arm and a pulse. If you are taking a prescription medecine for anxiety, a polygrapher will no doubt tell you to keep on taking it, and will proceed with the polygraph as if you had no anxiety disorder.

2) If you should ever need to take a polygraph for a job, you should educate yourself about polygraphy beforehand. Polygraph "testing" has not been proven to reliably detect deception at better than chance levels of accuracy in people without a serious medical condition, let alone those who do. You'll find an expose of polygraphy along with tips on how to reduce the risk of a false positive outcome in The Lie Behind the Lie Detector.

This is a very nasty area. Apart from countermeasures, psychological and phsiological conditions/treatments can alter autonomic reactions. In reviewing recent literature, there are conditions (everything else being the same) which enhance the polygraph response as well as those that  interfere with a "valid" response. The conditions/treatments of most interest are those that  generate false-positives ("failing" an otherwise innocent person) and false-negatives (possibly allowing a terrorist through). 

If the polygraph is only being used as an "excuse" to frighten weak minds into a confession, then the authorities don't really care about any medical conditions because accuracy doesn't count at all.  When an attempt is being made to use the polygraph "responsibly" as an investigative tool - treatments and illness matter, for example:

"Sec.  709.5  Waiver of polygraph examination requirements., (a) General. The CI-scope polygraph examination requirement under Sec.  709.3 of this part does not apply to:
...
(2) Any individual who is being treated for a medical or 
psychological condition that, based upon consultation with the  individual and appropriate medical personnel, the Secretary or the  Director of the Office of Counterintelligence determines would preclude  the individual from being tested;...",Federal Register: January 7, 2005 (Volume 70, Number 5) Proposed Rules, Page 1383-1396,DEPARTMENT OF ENERGY,10 CFR Parts 709 and 710,...Counterintelligence Evaluation Regulations, http://www.fas.org/sgp/news/2005/01/doe010705.html

"3.4 Polygraph Examinee
3.4.1 The examiner shall make reasonable efforts to determine that the examinee is a fit subject for testing, where allowed by law. Basic inquiries into the medical and psychological condition of the examinee as well as any recent drug use should be made where allowed by law. Mental, physical or medical conditions of the examinee that should be observable to, or that should be reasonably known by the examiner, should also be evaluation prior to testing. No test should be conducted where valid results could not be reasonably foreseen.
3.4.2 During the pretest interview, where allowed by law, the examiner will specifically inquire of the person to be examined whether or not he or she is currently receiving or has in the past received medical or psychiatric treatment or consultation.
3.4.3 If an examiner has a reasonable doubt concerning the ability of an examinee to safely undergo an examination, a release from the examinee and his or her physician shall be obtained.", American Polygraph Association, Standards of Practice, http://www.polygraph.org/standards.htm

“In those instances when the examinee is undergoing treatment by a medical or mental health professional, coordination with the attending medical or mental health professional is essential to evaluate the examinee’s overall suitability and to obtain medical clearance to conduct PDD testing. This form of coordination is also necessary to ensure that PDD testing does not interfere with ongoing treatment efforts and to prevent PDD testing of an otherwise unsuitable examinee.
Psychological Suitability: Polygraph testing of an examinee receiving current, on-going treatment and/or prescribed medication by mental health professionals (psychiatrist, psychologist, mental health counselors or other mental health professionals) shall be discontinued or postponed until the examinee’s attending mental health professional declares the individual suitable for PDD testing. Verbal authorization from the attending mental health professional is permitted, but should be the exception and not the rule. In instances where the examinee cites mental health related illnesses associated with severe depression or other severe illnesses, written authorization from the attending mental health professional is mandatory. Any questions concerning an examinee’s psychological suitability for PDD testing must be addressed with the attending mental health professional and/or a CRC supervisor prior to PDD testing.
Physiological Suitability: Polygraph testing of an examinee being treated and/or prescribed medication by medical professionals (doctors, physician assistants, nurses, or other medical specialist) for significant injuries or illnesses shall be postponed until the examinee’s attending medical professional declares the individual suitable for PDD testing. Verbal authorization from the attending medical health professional is permitted, but should be the exception and not the rule. In instances where the examinee cites severe medical illnesses, written authorization from the attending medical professional is mandatory. Any questions concerning an examinee’s physiological suitability for PDD testing must be addressed with the attending medical professional and/or a CRC supervisor prior to PDD testing.”, FORENSIC PSYCHOPHYSIOLOGICAL DETECTION OF DECEPTION(PDD) POLICY AND PROCEDURE MANUAL, Section 8.12 Examinee Suitability,  UNITED STATES ARMY CRIMINAL INVESTIGATION COMMAND, Effective 21 February 2005

"Other Psychopathology
Guilty psychopaths may escape detection because they are not concerned enough about a misdeed to create interpretable physiological responses. Individuals with other forms of psychopathology may escape detection or be classified as false positives for other reasons (e.g., emotional instability, delusional thinking). The one study that has investigated this possibility (74) found, in fact, that innocent neurotics and particularly psychotics were likely to be identified as deceptive. There were no guilty subjects in this “real crime" analog study.",Scientific Validity of Polygraph Testing: A Research Review and Evaluation - A Technical Memorandum, U.S. Congress, Office of Technology Assessment , Washington D.C., OTA-TM-H-15, November 1983 – Chapter 6 Factors Affecting Polygraph Examination Validity - Other Psychopathology

etc...

I am not an attorney so I can't give any legal advice, I think the following information would be useful to anyone with psychological disorders applying to one of the agencies that screen with the polygraph.

Personnel Security Standards and Procedures Governing Eligibility for Access to Sensitive Compartmented Information (SCI), DCID 6/4: section 4.a, section 7.e, Annex A - Section 13.o , supports that an agency can require you to take a polygraph as part of a background investigation for TS/SCI even though it's not a requirement from the DCI for  TS/SCI. (this should now be the DNI). Even then using it for screening purposes is unethical and a violation of executive orders, because the guidelines that allow them to use the polygraph also state that a person must be adjudicated based on a "whole person" concept(Annex B - Section 2,  Annex C - Section B.1 ). 

The one escape clause is that if an agency discovers during the course of its investigation that you have some massive security related defect then they can terminate  your processing (Annex C, Section B.4).

However, in the case of someone with a psychological disability such as anxiety disorder,  that causes them to have a greater than average chance of "failing" a polygraph, it would be illegal discrimination under the ADA (read rehabilitation act of 1973 for Federal agencies) to use the results of the polygraph as a screen no matter what the results are. 

That's because unless the ability to "pass" a polygraph is related to the duties of the position (e.g. you are a tester for polygraph machines), a disabled person cannot be screened out on the basis of a polygraph test or any other test unrelated to job duties. 

Agencies can get out of this requirement if they can show that compliance with the law would be undo hardship. Based on the small number of cases that would actually have to be fully adjudicated and the current trouble this administration is already having due to the Patriot Act, it would seem impolitic to publicly deny the disabled equal opportunity in an election year.

  Its very comforting to know I'm not the only one with an anxiety disorder.  I have obsessive compulsive anxiety disorder. Basically I look for something to stress about, until I deal with it.  I take lexapro.  Anyway I took a test a couple of months ago an got an inconclusive.  So I retook the test recently and again got an inconclusive.   
  I didn't lie and didn't use CMs.  The polygrapher believes its the medication.  I'm now waiting to see how my p.o. deals with it.  What are my rights?  Should I be scared of some kind of punishment or restrictions due to a medical condition.  I should note I have passed every previouse test before starting medication.

Off-Topic replies have been moved to this Topic.

Sarah,

As I noted above, polygraph "testing" has not been proven to reliably detect lies at better than chance levels of accuracy in people without a serious medical condition, let alone those who do.

It's certainly possible that your anxiety contributed to your failing the polygraph, but trying to determine why one failed an invalid procedure such as a polygraph "test" is akin to trying to determine why a coin toss came out heads instead of tails.

DarrellGi,

I think the best thing you can do to lower your anxiety is to educate yourself about the polygraph process and to learn what to expect and what can be done to mitigate the risk of a false positive outcome. To that end, I recommend that you review Chapters 3 & 4 of The Lie Behind the Lie Detector.