The aim of this study was to compare the efficacy of single-dose pefloxacin 400 mg and ciprofloxacin 250 mg in the treatment of acute uncomplicated gonococcal urethritis in males. One hundred and twenty male patients with uncomplicated gonococcal urethritis were assigned alternately to receive single oral doses of either pefloxacin 400 mg or ciprofloxacin 250 mg. Forty-one out of 43 patients (95.3%) of the pefloxacin group and 46 of 47 (97.9%) of the ciprofloxacin group were cured of gonorrhoeae. The rates of post-gonococcal urethritis were 57.7% and 53.3% in the pefloxacin and ciprofloxacin groups respectively. There was a high incidence of penicillinase-producing gonococci (34.2%). High level resistance to pefloxacin (minimum inhibitory concentration [MIC] >1.0 mg/l) resulting in clinical failure on 400 mg stat dose was noted in 1 isolate. It also showed decreased susceptibility to ciprofloxacin (MIC 0.25 mg/l). Another isolate showed high-level resistance (MIC 0.06 mg/l) to ciprofloxacin 250 mg stat dose with concomitant decreased susceptibility to pefloxacin (MIC >1.0 mg/l). Ciprofloxacin 250 mg stat dose is still useful for the treatment of uncomplicated gonococcal urethritis in males. The cure rate of 95.3% with pefloxacin at 400 mg stat dose is acceptable, but needs to be monitored with caution. The emergence of a more resistant strain of Neisseria gonorrhoeae to fluoroquinolones calls for vigilance in the monitoring of antimicrobial susceptibility.