HLA-DM and HLA-DO are non-classical MHC class II genes and modulate the peptide loading to the classical MHC class II proteins inside endosomes. While HLA-DM catalyzes the peptide-exchange in favor to a highly stable MHC class II/peptide-complex, HLA-DO acts as its natural antagonist. However, only few alleles of the HLA-DM/DO genes HLA-DMA, HLA-DMB, HLA-DOA and HLA-DOB are known and data about allelic frequencies or functional differences are sparse. Therefore, the aim of this study was to provide an overview about their allelic diversity using nanopore sequencing on 1880 samples from potential stem cell donors registered with DKMS Germany, DKMS UK, DKMS Poland and DKMS Chile.