Background Adapted treatments for Helicobacter pylori infection, guided by determining antimicrobial resistance, are associated with high eradication rates. We evaluated the performance of the Amplidiag® H. pylori + ClariR PCR assay (Amplidiag®) for detecting H. pylori and its clarithromycin resistance from gastric biopsies taken during endoscopy in comparison to culture and our “in‐house” PCR. Materials and Methods A total of 127 gastric biopsies were analyzed (98 adults; 29 children). Culture, PCR Amplidiag®, and in‐house PCR were performed in parallel. The in‐house PCR combined amplification and sequencing of a 267‐bp fragment of the H. pylori 23S rRNA gene. Discrepancies were controlled by amplification of glmM gene. Results For detection of H. pylori, Amplidiag® and the in‐house PCR were concordant in 118 of 127 of cases: 66 negative and 52 positive. Discrepancies were observed in nine cases, all with low bacterial load: Amplidiag® did not detect seven biopsies positive on in‐house PCR but detected two positive biopsies that were negative on in‐house PCR. Among the 19 of 52 (36%) H. pylori cases resistant to clarithromycin, only four biopsies with mixed populations exhibited discordant results between the two PCR methods. The A2142T mutation was not detected by Amplidiag®. With the in‐house PCR and amplified glmM gene as the reference method, the sensitivity and specificity of Amplidiag® was 88.5% (95% confidence interval 83‐94.1) and 100%. Conclusion This study demonstrated the high sensitivity of the PCR‐based Amplidiag® H. pylori test, especially with low H. pylori load, and the probability of its clarithromycin resistance analysis. For clinical use, a well‐designed trial with a large scale of samples may still be needed.