Background and Aim: The present study was designed to determine the eradication rate of 10day sequential therapy in genotypic clarithromycin-resistant Helicobacter pylori group identified by molecular polymerase chain reaction (PCR) detection in Thai patients. Methods: Between May 2007 and June 2010, patients who had undergone gastroscopic examination at the King Chulalongkorn Memorial Hospital, for dyspeptic symptoms were recruited. Two biopsy samples from gastric antrum were obtained, one for rapid urease test and another for PCR. PCR-sequencing was performed to determine point mutations in 23S rRNA gene. Patients received 10day sequential therapy consisting of lanzoprazole 30mg and amoxicillin 1 g twice daily for 5days followed by lanzoprazole 30mg, clarithromycin 500mg and nitroimidazole 500mg twice daily for the remaining 5days. Urea breath test (UBT) was performed to assess eradication therapy. Results: A total of 151 patients (mean age 52.7years, 75 males and 76 females) were recruited in this study. All patients completed sequential therapy without significant side effects. Point mutations at A2143G and A2142G were detected in 17 patients (11.3%). Overall eradication rate was 94%. The eradication rate in the group with point mutation was significantly lower than the eradication rate in the group without point mutation (64.7% vs 97.8%; odds ratio=19.6 and 95% confidence interval=4.3-88.8; P<0.0001). Conclusion: Genotypic clarithromycin resistance was detected in only 11.3% of H. pylori infections in Thailand. Sequential therapy is highly effective in clarithromycin-sensitive but is less effective in clarithromycin-resistant H. pylori. PCR-molecular test could be a useful tool to identify antimicrobial resistance for optimizing an eradication regimen. © 2011 Journal of Gastroenterology and Hepatology Foundation and Blackwell Publishing Asia Pty Ltd.