Metronidazole resistance is an important factor related to failure in the treatment of Helicobacter pylori. The mutation in the rdxA and frxA genes is the most important cause of resistance to metronidazole. Since the resistance rate of metronidazole is high in our region, we decided to assess the frequency of these mutations among H. pylori clinical isolates. Antral gastric biopsy specimens were cultured and minimal inhibitory concentrations (MICs) of metronidazole were determined by the E-test method. The rdxA and frxA genes were amplified in all isolates through the use of PCR with the specific primers. PCR products were purified for sequencing. The resultant sequences were compared with the wild type reference sequences to find any possible mutations. According to our findings, the rate of metronidazole resistance was 77%, with the MICs ranging from 0.25-1 µg/ml for metronidazolesensitive group and from 16-256 µg/ml for resistance group. H. pylori isolates containing a single mutation in rdxA or frxA genes demonstrated a low MIC (8-16 µg/ml), while those containing mutations in both genes showed a higher MIC (32-256 µg/ml). In this study, all resistant H. pylori isolates contained single or multiple nucleotide substitutions in the mentioned genes. Nevertheless, no nucleotide substitutions were found in the sensitive clinical isolates. The results of our study showed that the mutations in rdxA are mostly related to metronidazole resistance, and mutations in frxA are able to enhance H. pylori resistance.