Genotypic, or DNA-based, methods have become increasingly applicable for infectious disease diagnosis and epidemiologic analysis. The ability to assess the pathogen's genotype directly bypasses requirements for cultivation and may diminish diagnostic delays with fastidious organisms. Genotypic typing methods have enhanced epidemiologic studies by providing techniques with greater discriminatory ability and smaller proportions of nontypeable samples. Hence, these methods enable rigorous studies to be performed regarding the nature of disease outbreaks. Phenotypic, or conventional, methods will remain important in diagnostic microbiology, especially with organisms that are relatively easy to culture. However, genotypic methods may become increasingly prominent in clinical microbiology laboratories, particularly with respect to diagnosis of fastidious pathogens, because of their relative speed, versatility, and lack of cultivation requirements.