This study was planned in order to investigate the presence of H. pylori by culture, Gram stain and PCR in gastric biopsy specimens obtained by endoscopy, and by PCR in stool specimens from the patients with upper gastrointestinal tract complaints and to compare the results obtained from the used methods. Two biopsy specimens were taken from the antrum of the patients, one of which was used for culture and Gram stain, and the other for PCR. Brucella agar (Biolab®, BAB20500) enriched with 5% sheep blood media was used for isolation of H. pylori. To obtain the DNA of H. pylori “NucleoSpin® Genomic DNA kit from biopsy specimens and “Invisorb® Spin Stool DNA kit (Invitek)” from stool specimens were used. PCR was performed by using Applied Biosystem 5700 Real Time PCR machine. The sensitivity and specificity of the used methods were calculated using Receiver Operating Characteristic (ROC) curve according to biopsy cultures results. Using the biopsy cultures as the “gold standard” test for determining H. pylori presence, the sensitivity and specificity of PCR was measured as 92.0 % and 72.7 % in the biopsy specimens, as 68.0% and 72.7% in the stool specimens and as 88.0% and 63.6% for Gram stain of biopsy specimens, respectively. It is concluded that Gram staining when it is evaluated with endoscopical findings of patients may be preferable for the diagnosis of H. pylori because it is easily applicable, rapidly conclusive, more inexpensive than the others, and has specificity as in PCR in the biopsy specimens.