The definitive identification of sexually transmitted pathogens has become increasingly important as their incidence has increased and their presence has been linked to transmission of human immunodeficiency virus. In the detection of pathogen-specific DNA, DNA probes and the polymerase chain reaction have tremendous theoretical advantages over traditional diagnostic methods in terms of sensitivity and automation. These new methods have been applied to the detection of human papillomavirus,Neisseria gonorrhoeae, syphilis, chancroid,Chlamydia trachomatis, andTrichomonas vaginalisamong others. However, despite these advantages, the problems with specificity and positive predictive values, as well as increased costs, have limited the broad application of molecular methods in most situations. Continued development of newer detection systems and comparison with existing methods will be needed to determine the proper utilization of molecular diagnostic methods in sexually transmitted diseases.