Commercially available nucleic acid amplification tests (NAATs) for Neisseria gonorrhoeae and Chlamydia trachomatis detection allow for self-collection including home-based collection from multiple anatomic sites such as the urethra, cervicovagina, rectum, and pharynx. Verification studies need to be done prior to processing pharyngeal and rectal specimens. We review specimen collection and test characteristics of NAATs at different anatomical sites.