Susceptibility testing was conducted on 1357 isolates of Neisseria gonorrhoeae isolated from 1993 through 2002 in Japan to assess the antimicrobial resistance. Selected isolates were characterised by auxotype and analysis was done for mutations within the quinolone resistance-determining region (QRDR) in the gyrA and parC genes, which confer fluoroquinolone resistance to the organism. Isolates with ciprofloxacin resistance increased significantly from 6.6% (1993-1994) to 73.5% (2002). The proportion of plasmid-mediated penicillin-resistant isolates (PPNG) decreased significantly from 7.9% (1993-1994) to 0.9% (2002). The percentage of chromosomal-mediated resistance to penicillin decreased from 27.4% in 2000 to 12.0% in 2001 but increased to 28.9% in 2002. The proportion of isolates with any type of resistance to tetracycline decreased from 24.7% in 2000 to 13.9% in 2001 and then increased to 22.3% in 2002. The proportion of prototrophic isolates significantly decreased from 84.4% in 1992-1993 to 7.7% in 2001, while that of the proline-requiring isolates significantly increased from 4.4% in 1992-1993 and 80.8% in 1998. The proline-requiring isolates were less susceptible to ciprofloxacin than the prototrophic or arginine-requiring isolates. Of 87 isolates resistant to ciprofloxacin, 2 (2.3%) contained five amino acid substitutions within the GyrA and ParC proteins, 76 (87.4%) contained three or four amino acid substitutions and 9 (10.3%) contained one or two amino acid substitutions.