Objective The aim of this study was to survey the antibiotic resistant pattern of H. pylori infection in different geographical locations in Thailand and to determine factors associated with antibiotic resistance. Methods A total of 3,837 dyspeptic patients who underwent upper endoscopy from different regions (North, Northeastern, Central and Southern) of Thailand during January 2005–March 2011 were enrolled in thisstudy. Two antral gastric biopsies were obtained for culture and susceptibility tests were performed using E-test. Results 1,327 patients (34.6%) were infected with H. pylori identified by rapid urease test. E-test for all 4 antibiotics was successful in 374 isolates (152 male, 222 female, mean age 48.7 years). The endoscopic findings demonstrated 301 gastritis patients and 73 peptic ulcer patients. The prevalence of antibiotic-resistant H. pylori was amoxycillin 5.6%, tetracyclin 1.9%, clarithromycin 3%, metronidazole 47.1%, and multidrugs 5%. In amoxycillin, clarithromycin and metronidazole resistant strains, age > 40 years was signifi cantly higher than age < 40 years (90% vs 10%; P-value = 0.04, 100% vs 0%: P-value = 0.03 and 65% vs 35%: P = 0.02 respectively). Conclusion Prevalence of H. pylori infection has decreased in all regions of Thailand. The prevalence of metronidazole resistant strain was high and remains the most common antibiotic resistant strains in Thailand whereas clarithromycin resistance has markedly declined in recent years. The reason for such a decline is likely due to the wide use of other newer antibiotics in place of clarithromycin. Age > 40 years might be a predictor for amoxycillin, clarithromycin and metronidazole resistant strain in Thailand.