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Background. An increasing resistance of Helicobacter pylori strains to antimicrobial agents is the serious therapeutic problem. The aim of this study was to compare the primary and secondary resistance of H. pylori strains isolated between 2006–2008 (data published) and 2009–2011 to clarithromycin and levofloxacin. Material and Methods. 220 dyspeptic patients (153 before treatment, 67 after), were enrolled in the study. 51 H. pylori strains were isolated. MIC values of clarithromycin and levofloxacin were determined by the E-test method. The statistical analysis was conducted with the χ 2 test with Yates correction at the 0.05 significance level (P ≤ 0.05). Results. Between 2006 and 2008, 34% (39/115) of H. pylori strains were resistant to clarithromycin (primary 21% (19/90), secondary 80% (20/25)). 5% (6/115) of strains were resistant to levofloxacin (primary 2% (2/90), secondary 16% ((4/25); data published) Between 2009–2011, 22% (11/51) of H. pylori strains were resistant to clarithromycin (primary 19% (8/43), secondary 38% (3/8)). 16% (8/51) of strains were resistant to levofloxacin (primary 12% (5/43), secondary 38% (3/8)). Conclusion. The present study has shown the increasing amount of resistant H. pylori strains isolated from patients in Southern Poland to levofloxacin and decreasing number of resistant strains to clarithromycin.