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I haven't heard of the NSA routinely checking applicants' Internet activity, and it seems doubtful that it would be practical to do so. However, during the pre-employment polygraph interrogation, you can expect to be asked about past crime, including on-line illegality. In this context, minor admissions may be blown out of all proportion, as the experience of "Frustrated" illustrates:
I was wondering, do the intelligence agencies (specifically the NSA) check previous internet activity when running background checks? I know it is possible that they could (if they wanted) easily track an applicant to his/her ISP and get the records that way, but is this a standard check for background investigations?