Helicobacter pylori strains isolated from different regions of the world or human ethnic groups exhibit some differences at certain loci. The aim of this study was to determine allelic differences of H.pylori strains isolated from two countries, Turkey and Germany. A total of 72 H.pylori isolates, of which 37 strains were from Kocaeli province of Turkey and 35 strains from Hamburg, Germany were included in this study. H.pylori strains had been isolated from gastric biopsies of the patients. Genomic DNA was extracted with phenol-chloroform-isoamyl alcohol procedure and vacA alleles and cagA regions were identified by polymerase chain reaction (PCR) using specific primer sets. The rates of cagA positivity in Kocaeli and Hamburg strains were found as 75.7% (28/37) and 71.4% (25/35), respectively. VacA s1a allele was predominant both in Turkey and Germany isolates. There were five vacA mosaicisms in Hamburg strains, including 14 for s1a/m1a (40%), nine for S1a/m2 (25.7%), eight for s2/m2 (17.1%), three for s1a/m1 (8.5%) and three for s1b/m2 (8.5%). There were four vacA mosaicisms in Kocaeli strains, including 22 for s1a/m2 (59.4%), eight for s2/m2 (21.6%), four for s1a/m1 a (10.8%), and three for s1a/m1 (8.1%). In this study, Hamburg and Kocaeli strains did not reveal significant differences regarding cagA status and vacA s1 allele. Whereas vacA s1a/m1a, cagA(+) type was the most frequent in Hamburg strains and s1a/m2, cagA (+) type in Kocaeli strains.