Neisseria gonorrhoeae was isolated simultaneously from urethral and pharyngeal specimens of two gonorrhea patients. The pair of isolates from one of the two patients were identical in auxotype, pulsed-field gel electrophoresis pattern, and antimicrobial susceptibility, which indicated that both sites in that patient were infected with the same strain of N. gonorrhoeae. However, the two isolates from the other patient had different properties, indicating that the two sites in the second patient were infected with different strains. The gonococcal infections in these patients failed to respond to initial treatment with sparfloxacin or sulbactam/ampicillin, because the causative strains of N. gonorrhoeae were resistant to the respective antibiotics. Variable patterns and routes of gonococcal infection have recently been discovered in individual patients, suggesting that specimens for bacterial isolation should be taken not just from one site but from various sites that might be infected. This method may contribute to the successful treatment and epidemiological investigation of gonococcal infections.