In this study we assessed minimum inhibitory concentration (MIC) values and resistance rates of several antibiotics in 65 primary and 324 secondary Helicobacter pylori isolates from Korean patients. Primary resistance to amoxicillin, clarithromycin, metronidazole, tetracycline, azithromycin, ciprofloxacin, levofloxacin and moxifloxacin was 18.5%, 13.8%, 66.2%, 12.3%, 32.3%, 33.8%, 21.5% and 21.5%, respectively. Secondary resistance was 31.3%, 85.1%, 70.1%, 0%, 89.6%, 35.8%, 32.8% and 32.8%, respectively. Sequence analysis of pbp1A in H. pylori strains with an amoxicillin MIC >or=2 microg/mL revealed C206T (Asp69-->Val), C1667G (Thr556-->Ser), A1684T (Asn562-->Tyr), A1777G (Thr593-->Ala) and C1798A (Pro600-->Thr) substitutions. Eleven (16.4%) of 67 treatment failures showed mixed infections with antibiotic-susceptible and -resistant H. pylori. The most common multidrug resistance profile was to clarithromycin, metronidazole and azithromycin. These results indicate that MIC values of secondary isolates were higher than those of primary isolates and that resistance to amoxicillin is probably mediated through mutations in pbp1A.