Colonization with Helicobacter pylori (HP) may have major clinical consequences and HP virulence factors are associated with more severe gastroduodenal pathologies. In this study, prevalence of HP in patients with Non-Ulcer Dyspepsia (NUD) was determined by rapid urease test and culture and correlations of histopathologic changes with bacterial virulence factors and serologic profiles were investigated. Gastric biopsies from sixty-nine patients admitted to Haydarpasa Training Hospital Department of Gastroenterology were evaluated for rapid urease, HP isolation and examined histopathologically. PCR was employed for HP confirmation and detection of HP cagA, cagE and virB11 genes. For each patient, IgG and IgA antibodies and anti-cagA antibodies were also determined by ELISA tests. HP was isolated and confirmed by PCR in 74% (51/69) of the patients. Anti-HP IgG and IgA were detected in 96% (49/51) and 53% (27/51), respectively. Anti-cagA were present in 51% (26/51). cagA, cagE and virB11 were positive in 56.8% (29/51), 60.7% (31/51) and 58.8% (30/51) of the patients, respectively. Statistically significant correlation was observed between cagA PCR and inflammation/activity scores. Detection of cagA by molecular assays can be an alternative test that can be employed for individual patient assessment.