Gonorrhea is a sexually transmitted disease; it is the most frequently reported infectious disease in the United States (12). Humans are the natural host of the etiological agent, Neisseria gonorrhoeae, which usually causes uncomplicated infections of mucous membranes of the urethra, cervix, rectum, or pharynx (24). Under certain conditions, the organism may disseminate and cause complicated infections such as pelvic inflammatory disease or disseminated gonococcal infection (DGI) (24). Although the incidence of reported gonococcal infections in the United States has decreased over the past 10 years to approximately 375 cases per 100,000 population, the incidence of infections caused by antimicrobial resistant strains has increased (13). With the recent development of typing techniques, it has been possible to characterize strains of N. gonorrhoeae phenotypically, determine epidemiological correlates of their pathogenicity and antimicrobial susceptibilities, and devise and evaluate strategies to control outbreaks of gonorrhea caused by specific strains. Previously, we have reviewed the applications of phenotypic characterization of N. gonorrhoeae strains to studies of reinfection versus treatment failure, coinfection, and forensic investigations; These will not be covered below (34). This review will discuss the methods used to characterize gonococcal isolates and their application to describe strain populations and determine epidemiological correlates of gonococcal infections. The bibliography for this review is extensive but selective and provides key references that will guide the reader to additional readings in this subject.