The highly polymorphic Major Histocompatibility Complex (MHC) genes are responsible for the binding and cell surface presentation of pathogen- or cancer-specific T-cell epitopes. The MHC Motif Atlas helps visualize, analyse, and compare the different binding specificities of thousands of class I and class II MHC molecules, and includes binding motifs, peptide length distributions, motifs of phosphorylated ligands, multiple specificities, or links to X-ray crystallography structures.