NAATs have been cleared by FDA for testing of genital specimens (cervical and male urethral swabs and urine), but the performance of NAATs has not been adequately evaluated for diagnosis of C. trachomatis and N. gonorrhoeae infections occurring at rectal or pharyngeal sites of sexual exposure. Increasing numbers of heterosexual individuals might be engaging in orogenital or rectal sexual activity, especially adolescents and young adults who might view such exposures as less risky with respect to pregnancy and sexually transmitted diseases (STD) than penile-vaginal intercourse. Pharyngeal and rectal exposures, often without use of condoms, are relatively common among MSM. Recent demonstration of resurgent sexually transmitted diseases and unsafe sexual practices among men-who-have-sex-with-men (MSM), including those who are infected with the human immunodeficiency virus (HIV), provides an especially strong public health imperative to the need for careful evaluation of NAATs with pharyngeal and rectal specimens.