Introduction Rapid development of Neisseria gonorrhoeae resistance to several antibiotics in recent years threatens treatment and prevention. Targeted surveillance of new resistance patterns and insight into networks and determinants are essential to control this trend. Methods Since the Gonococcal Resistance to Antimicrobials Surveillance (GRAS) project was implemented within the Dutch national sexually transmitted infection (STI) surveillance network in July 2006, participating STI centres have collected a culture from each gonorrhoea patient. Isolates were tested for susceptibility to penicillin, tetracycline, ciprofloxacin and cefotaxime using Etest. Logistic regression was used to determine risk factors for ciprofloxacin resistance. Results Between July 2006 and July 2008, prevalence of resistance to penicillin was 10%, to tetracycline 22% and to ciprofloxacin 42%. Resistance to cefotaxime was not found, although minimum inhibitory concentrations higher than 0.125 mg/l drifted upward (p<0.05). Ciprofloxacin resistance rose from 35% in 2006 to 46% in 2008 (p<0.05), despite 2003 guidelines naming cefotaxime as first-choice therapy. In men, ciprofloxacin resistance was higher in men having sex with men (MSM) than in heterosexual men (adjusted OR 2.0, 95% CI : 1.5 to 2.6). In women, it was higher in commercial sex workers (adjusted OR 25.0, 95% CI 7.7 to 78.2) and women aged over 35 years (adjusted OR 8.2, 95% CI 3.0 to 22.7) than in other women. Conclusion Ciprofloxacin resistance in The Netherlands is increasing, and is particularly found in MSM, older women, and female sex workers. No resistance to current first-choice therapy was found, but alertness to potential clinical failures is essential. By merging epidemiological and microbiological data in GRAS, specific high-risk transmission groups can be identified and policy adjusted when needed.