Objective: The difficulty of growing of Helicobacter Pylori (H.pylori) under in vitro conditions decreases sensitivity of diagnostic methods based on bacterial isolation. However, the PCR method targeting glmM (formerly ureC) gene of bacteria was shown as an alternative to culture in many studies. The aim of our study was to compare these two methods, as well as to determine the effect of gastric localization of H.pylori on sensitivity and applicability of these methods. Material and Methods: This study included two antral and two corpus biopsy samples obtained from 231 patients (158 with gastritis and/or gastric ulcer and 73 with duodenal ulcer) without prior treatment for H.pylori. One antral and one corpus sample were cultuvated in modified Columbia agar media containing horse blood (7%) and antibiotics for H.pylori isolation. The other samples were investigated by PCR assay using specific primers for H.pylori glmM gene sequences. Results: H.pylori was detected by culture method in 163 (70.6%) and by glmM-PCR method in 201 (87.0%) of 231 antral biopsy samples (p< 0.001, x(2) test). The numbers of H.pylori-positive corpus samples were found as 97 (42.0%) and 154 (66.7%), respectively (p< 0.001, X-2 test). Assuming glmM-PCR method which have higher positivity on the diagnosis of H.pylori as the gold standard, specificity of culture for both sample groups were 100%, however, its sensitivity was detected as 81.1% for antral samples and 63.0% for corpus samples. Conclusion: Our results indicate that culture method is less sensitive for diagnosis of H.pylori-related gastroduodenal diseases; its sensitivity decreases to 58.4% in corpus biopsy samples obtained from the patients with corpus predominant gastritis and/or gastric ulcer.