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Background and Aims: We found a higher incidence of myocarditis in young males who had received at least two Pfizer‐BioNTech BNT162b2 vaccinations. The human leukocyte antigens (HLA) are known to play an important role in infectious and autoinflammatory diseases. We hypothesized that certain HLA alleles might be associated with vaccination‐induced myocarditis. Methods: HLA typing was performed using next‐generation sequencing technology with the Illumina Iseq100 platform. HLA class I and II loci were genotyped in 29 patients with post‐vaccination myocarditis and compared with HLA data from 300 healthy controls. Results: We demonstrate that the DRB1*14:01, DRB1*15:03 alleles and the motifs in HLA‐A − Leu62 and Gln63, which are part of binding pocket B and HLA‐DR Tyr47, His60, Arg70 and Glu74, which are part of binding pockets P4, P7 and P9, were significantly associated with disease susceptibility. Conclusions: Our findings suggest that immunogenetic fingerprints in HLA peptide‐binding grooves may affect the presentation of peptides derived from the Pfizer‐BioNTech BNT162b2 vaccination to T cells and induce an inflammatory process that results in myocarditis. [ABSTRACT FROM AUTHOR]