A novel method for genotyping the clustered regularly interspaced short palindromic repeat (CRISPR) locus of Campylobacter jejuni is described. Following real-time PCR, CRISPR products were subjected to high-resolution melt (HRM) analysis, a new technology that allows precise melt profile determination of amplicons. This investigation shows that the CRISPR HRM assay provides a powerful addition to existing C. jejuni genotyping methods, and emphasizes the potential of HRM for genotyping short sequence repeats in other species.