Ciprofloxacin-resistant Neisseria gonorrhoeae had been rarely detected on Merseyside and when found was associated with beta-lactamase producing strains, imported from abroad. However, in August 2000, two cases of infection with ciprofloxacin-resistant beta-lactamase-negative strains occurred in sexually unrelated patients with no history of foreign travel. Over the next 18 months a total of 120 patients presented with ciprofloxacin-resistant gonococci, from which 99 patient strains were available for study. Gonococcal DNA was subjected to molecular fingerprinting by polymerase chain reaction amplification followed by Taq1 digestion of their opa genes. Twelve differing opa-types were found, but 79 patients were infected with a single genotype, opa-type 1. The sexual histories of the majority of this group indicated acquisition in Merseyside. This endemic strain was further characterized by having the same amino acid substitutions on gyrA and parC genes. An endemic clone of ciprofloxacin-resistant N. gonorrhoeae has been established on Merseyside necessitating the introduction of ceftriaxone as first-line treatment. Despite the presence of 11 other clones in the city, opa type-1 strains have not yet been displaced, raising the possibility that this strain is endowed with added virulence/endemicity traits or that a number of source patients have not yet been found.