Background/Aims: After the identification of Helicobacter pylori as a major cause of gastric and duodenal ulcer, special attention has been paid to this bacterium. The aim of this study is to prove the usefulness of the 16S rRNA polymerase chain reaction (PCR) assay as a diagnostic method of H. pylori infection in the gastric biopsy specimens and to investigate whether the severity of histological gastritis is related to the cagA. Methods: Biopsy specimens were obtained from the gastric antrum of 46 patients with chronic gastritis during endoscopy. Histological examination, CLO test and PCR using 16S rRNA and cagA primer were performed. Results: The 16s rRNA PCR were positive in 27 out of 28 infected patients, and negative in 3 out of 18 not-infected patients. The sensitivity of 16S rRNA test for the diagnosis of H. pylori infection was 96.4% and the specificity was 83.3%. The degree of chronic inflammation and activity were more severe in the H. pylori infected patients than in the not-infected controls (p<0.05). No significant difference in histological parameters was noted between cagA positive and cagA negative groups. Conclusions: The 16S rRNA PCR is a highly sensitive but somewhat less specific test for the diagnosis of H. pylori infection. We suggest that careful cleansing and minimization of the contamination can make PCR clinically useful test. PCR recognition of cagA was not associated with the severity of H. pylori gastritis. (Korean J Gastroenterol 1998;31:281-289)