I failed one poly with a 3 letter agency under DOJ. I am in the process of taking a poly with 2 more under DOJ. I was not told why I failed the poly. But I do think the polygrapher failed me because he thought I wasn’t being truthful about crime committed either in my adulthood or when I was younger 
. I currently have a secret clearance with a 3 letter agency under DHS. Would that fail polygraph affect my chances since those agencies are under DOJ?
Can’t say for sure but I have met several people who ‘failed’ a poly with Agency X only to later pass a poly and get hired by Agency Y, in some cases both X and Y fell under the Dept of Defense.
I think it may be a positive sign that you have gotten this far in the process that they will schedule a poly, since they undoubtedly know about the previous attempt.
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Thank you for sharing your knowledge
Yes, your prior failed polygraph will affect your chances with other agencies. When you go for your polygraphs, you’ll be asked about any prior polygraphs you’ve undergone and what the outcome was. When you disclose that you’ve previously failed a polygraph, that will tend to bias the polygraph operator against you, making your failing a second time more likely.
It seems like I did very well on the poly.
Congratulations! I’m glad to know that your prior polygraph did not determine the outcome of your subsequent one. 
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Things are moving well. Spousal interview has been completed and BI file has been submitted for review. I believe I will overcome my arrest issue since the agency is still pushing forward with my application. Again, I only talk to them once about my arrest and that was during the PSI. I am expecting to get some good news by next week or so.
I have summer internship with 3 letter agency under DOJ. I did the first phase a month ago which are the SP86, PSI, Polygragh and drug test. My packets are with Security Team, waiting for the security team do what do best. They’ve not contact any of my references yet and I have a deadline (1st May) or I will be discontinued from the program. How long did your reference interviews take and do you think they’ll complete everything before the deadline? 
From my experience, its didn’t take long at all. Within 4 weeks all my references, work, school were contacted. My investigator told my file has been submitted in for review about. At this point I don’t know if I am in adjudication or not.