Gonococcal isolates resistant to ciprofloxacin collected from 2004 to 2005, in the Pretoria region, were characterised using Neisseria gonorrhoeae multi-antigen sequence typing (NG-MAST). The isolates were obtained from men presenting with urethritis to primary healthcare clinics and general practitioners. All isolates were tested for susceptibility to ciprofloxacin by Etest, disc diffusion and agar dilution methods. Sequence-based typing, directed at the por and tbpB genes, and compared with international isolates using the NG-MAST database on the internet, was done for 18 isolates (10 ciprofloxacin-resistant isolates and 8 susceptible controls). There was one cluster (four isolates) of known sequence type (ST) similar to the pattern seen among strains from Scotland, England, and Durban, South Africa. Two other known STs were identified, while the remaining STs were unique.