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Background Helicobacter (H.) pylori is primarily an extracellularly living bacterium. However, seemingly intracellular occurrence can often be detected by immunohistochemical stains. Considering antimicrobial resistance, we investigated the impact of the apparent intracellular H. pylori (aiHp) on treatment failure of first-line triple therapies. Methods Gastric biopsies of 814 H. pylori infected patients naïve for treatment were analyzed before and after eradication therapy by immunohistochemistry. Thereof, 373 received treatment consisting of amoxicillin, clarithromycin and PPI (AC/PPI). Availability of PCR-based clarithromycin susceptibility test results from pre-treatment gastric biopsies was a pre-condition for matching 52 aiHp to 52 non-aiHp cases within the AC/PPI-group. Results AiHp were detected mostly in low counts predominantly in corpus, rarely in antrum biopsies (95.2% vs. 24.6%); they were found in 497 (61%) of all patients and in 192 of 373 patients (51.5%) in the AC/PPI-group. The eradication rate in aiHp vs. non-aiHp cases was 44.4% vs. 72.9% in the entire sample and 45.3% vs. 66.8% in the AC/PPI-group. Among the 104 paired patients, respective values were 46.2% vs. 78.8%; in clarithromycin susceptible cases 60.6% vs. 91.9%. Both aiHp and resistance to clarithromycin proved to be highly significant (p≤0.001) and independent predictors of eradication failure. Twelve of 13 aiHp cases with a clarithromycin sensitive strain, who failed eradication, developed resistance to the antibiotic. Conclusions AiHp found by immunohistochemical staining especially in corpus biopsies proved to be a risk factor for failure of first-line triple therapies; occurrence of aiHp should be considered with regard to therapy options.