Purpose of this study was to compare the five different primer pairs (16S rRNA, random chromosome sequence, SSA gene, ureA and glmM ) for detection of the Helicobacter pylori (H. pylori) DNA in adenoid and tonsil tissues by polymerase chain reaction (PCR). Sixtyfive tissue samples from 26 patients were analyzed in this study. PCR was performed by using the DNAs obtained from clinical samples and the primers specific to five different gene regions. In the result of PCR method, the presence of H. pylori DNA was detected in 16 (24.61%), 15 (23.07%), 14 (21.53%), 10 (15.38%) and 7 (10.76%) of the 65 samples using 16S rRNA, glmM, SSA gene, random chromosome sequence and ureA primers, respectively. According to the data, we recommend use of 16S rRNA and glmM primers in the PCR method for detection of H. pylori in adenoid and tonsil tissues.