Objective: H.pylori infection is one of the most common bacterial infections worldwide. Its prevalence has been estimated to range from 40 to 80% and it varies widely by geographic area, age, race, ethnicity, and socioeconomic status. Since culture methods for isolation of H.pylori in gastric biopsy specimens were insensitive, time consuming and cumbersome, molecular methods for detection and typing of H.pylori are gaining importance. Many PCR methods have been developed to detect the organism directly in clinical specimens. The targets of these PCR methods include the 16S rRNA gene, the random chromosome sequence, the 26-kDa species-specific antigen (SSA) gene, the urease A (ureA) gene, and the phosphoglucosamine mutase (glmM) gene, formerly named urease C (ureC) gene. The aim of present study was to compared the sensitivities of two different PCR methods based on ureA and ureC for the detection of H.pylori in gastric biopsy specimens. Material and Methods: In our study, genomic DNA of 220 gastric biopsi samples (110 antral, 110 corpus) were extracted with QIAGEN tissue kit and H.pylori target genes (ureA and ureC) were amplified by PCR. Results: H.pylori ureC and ureA genes were found in 80.5 and 71.8 percent of biopsy samples respectively. Conclusion: It appears that ureC based-PCR is a useful primary tool to detect and is distinguish H. pylori strains from gastric biopsy specimens and it is superior to ureA based-PCR.