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Neisseria gonorrhoeae isolates exhibiting clinically significant resistance to fluoroquinolones have been isolated most frequently in Asian and western Pacific countries, including Thailand. In Bangkok, Thailand, ciprofloxacin has been used to treat gonorrhea since 1987.Our goal was to determine the prevalence of isolates of N gonorrhoeae that exhibit resistance to ciprofloxacin in Bangkok and to characterize these strains with regard to ciprofloxacin MICs, auxotype/serovar (A/S) classification, gyr A and par C mutations responsible for ciprofloxacin resistance, and outer membrane lipoprotein (Lip) subtype analysis.MICs of gonococcal isolates from consecutive patients attending the Bangrak Hospital STD Clinic in Bangkok were determined by agar dilution. A/S class was determined by established procedures. Mutations within gyr A and par C were determined by DNA sequencing. Lip subtypes were determined by PCR and DNA sequencing.In 1998 and 1999, 115 of 168 isolated strains of N gonorrhoeae exhibited decreased susceptibility or resistance to ciprofloxacin, and three cases of possible ciprofloxacin treatment failure were identified. Ciprofloxacin-resistant (CipR) strains increased from 13.8% (8/58) in 1998 to 25.4% (28/110) in 1999 (P = 0.08). Ciprofloxacin MICs of CipR isolates ranged from 1.0 μg/ml to 32.0 μg/ml. CipR strains belonged to a number of A/S classes and Lip subtypes. Different CipR strains contained alterations at both amino acid 91 and amino acid 95 of gyr A and also contained an amino acid alteration in par C. These alterations are known to be involved in gonococcal resistance to ciprofloxacin.The prevalence of CipR strains of N gonorrhoeae isolated in Bangkok increased substantially in the 1990s. Characterization of the CipR isolates revealed a number of different strain subtypes, indicating that CipR isolates in Bangkok are not from a single clonal source and therefore result from multiple cases of importation or local emergence. Because of the high level of CipR isolates at Bangrak Hospital, in 2000 the Thai Ministry of Public Health issued recommendations against the use of fluoroquinolones for the treatment of gonococcal infection in Thailand.