Yes, sometimes even tests can not always detect an STI.
For example: Lesions that are suspected to be Herpes can be swabbed and tested but may not come back as Herpes. Sometimes a blood test can be ordered to find out for sure.
However, with the correct testing for each STI there should be a correct result that is certain. Chlamydia and Gonorrhea should be tested from a swab cultures, viral STI's should be detected by blood.
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Most of the time herpes does show up on a test. If it's being tested for, the routine std tests don't always include a test for herpes.
Unless you just contracted it or don't have enough antibodies in your blood to show positive results then it may not show up.