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This study examined whether the simultaneous presence of metronidazole-susceptible and -resistant Helicobacter pylori colonies in a single biopsy specimen is caused by a multiple strain infection with a susceptible and a resistant strain or by two subpopulations within a single strain. Single colonies obtained from seven biopsy specimens known to harbour both susceptible and resistant Helicobacter pylori were fingerprinted by restricted fragment length polymorphism typing of the ureC gene and by the random amplified polymorphic DNA procedure. Metronidazole susceptibility was determined by the E test. The results indicated that the occurrence of metronidazole-resistant and metronidazole-susceptible bacteria within a single biopsy does not imply the presence of a multiple strain infection with one resistant and one sensitive strain.