Abstract: The aim of this study was to detect cytotoxin-associated gene A (cagA) and vacuolating cytotoxin gene A (vacA) genotypes of Helicobacter pylori and to study their relationships to the associated diseases. In the present analytical descriptive study H. pylori isolates were collected from 150 patients who underwent gastro duodenoscopy in Imam Khomeini Hospital of Tabriz, Iran. Of the patients 76 (50.7%) were males and 74 (49.3%) were females. The patients were divided into two groups. Group I consisted of 117 (78%) Non-Ulcerative Dyspepsia (NUD) patients and group II consisted of 33 (22%) Peptic Ulcer Disease (PUD) patients. Extracted DNA of H. pylori isolates were subjected to PCR tests to detect cagA, signal (s) and middle (m) regions of vacA genotypes. The designed primers revealed the presence of cagA gene in 125 (83.3%) of the isolates. Regarding vacA signal sequences 99 (66%) of our isolates revealed s1 type. The proportion of s1a, s1b and s1c subtypes were 76/150 (50.7%), 7/150 (4.7%) and 16/150 (10.6%), respectively while 40/150 (26.7%) presented as s2 type. In further analysis of the m region of vacA, m1 and m2 subtypes were detected in 49/150 (32.7%) and 81/150 (54%) of the isolates, respectively. The m1 subtype were further divided into m1a [41/49 (83.7%)] and m1b [(8/49 (16.3%)]. Thirty one isolates (20.7%) showed more than one vacA alleles in a single patient. Our results showed that isolates carrying the cagA gene were higher in PUD group than in NUD group, but did not substantiate statistically the role of cagA as a marker influencing increased virulence (p>0.05). Present findings also showed that s1 and s2 subtypes of vacA gene are markers which differentiate between PUD and NUD groups.