The aim of the study was to evaluate the prevalence of main virulence genes in Helicobacter pylori strains from H 6 patients with peptic ulcers (41 cases) and nonulcer diseases (75) by polymerase chain reaction (PCR) with pure cultures and to compare the results with those by multiplex PCR in 39 H. pylori-positive gastric biopsies in another center in Sofia, Bulgaria. Strain susceptibility to amoxicillin, metronidazole, and clarithromycin was determined by agar dilution method. By PCR with pure cultures, coinfections with multiple H. pylori strains were found in 8 (6.9%) patients who were excluded from the statistical analysis. Prevalence of toxigenic type vacA sl was higher (91.7%) than that usually reported in Europe. cagA-positive genotype was detected in most (81.5%) strains, and almost all of them harbored vacA sl genotype. Strains with cagA+/vacA sla genotype were more corm-non (80.6%) than the other genotypes (19.4%, P = 0.0001). The ulcer patients had more often virulent strains than the other patients (92.3% versus 75.4% for cagA+, 100.0% versus 87.0% for vacA sl, 100% versus 84.0% for vacA sla, and 92.3% versus 73.9% for cagA+/vacA sla, respectively). The prevalence of H. pylori virulence-associated genes was not associated with patients' sex and age or with the antibacterial resistance of strains. The most common H. pylori genotype was cagA+/vacA sla. Similar prevalence of cagA-positive (82.1%), vacA sl (97.4%), and cagA+/vacA sl strains (79.5%) was found by multiplex PCR in gastric biopsies in the 2nd center. In conclusion, H. pylori strains with virulent genotypes are widespread in symptomatic Bulgarian patients. (C) 2009 Elsevier Inc. All rights reserved.