Amplification methods for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in genitourinary specimens have changed the way in which routine Clinical Microbiology laboratories fulfill requests for recovery of these two common agents of sexually transmitted disease. PCR, strand displacement amplification, transcription mediated amplification and signal amplification (Hybrid Capture) are available as commercial products that can be used to assay endocervical, urethral, and urine samples from female and male patients for screening in high-risk asymptomatic patients as well as for diagnosis in the symptomatic patient. Although the methods differ, the overall results are increased sensitivity and rapid detection as compared to conventional means of detection of C. trachomatis and N. gonorrhoeae. There are some limitations to the use of amplification, for example, in cases of sexual abuse, in requests for a test-of-cure within 2-3 weeks of initial detection, and in non-genitourinary specimens. Use of the assays is beginning to change the epidemiology of these sexually transmitted diseases, especially in the increased numbers of C. trachomatis that have been reported to the Centers for Disease Control in the US over the past several years.