The polymorphic HLA-class II gene families HLA-DR, -DP, and -DQ on chromosome 6 are in strong linkage disequilibrium and inherited together as a haplotype. Nowadays, matching for HLA‐A, ‐B, ‐C, ‐DRB1, and -DQB1 loci (10/10 match) is the gold standard for unrelated hematopoietic stem cell transplantation (HSCT). However, there is increasing evidence that all class II loci affect HSCT outcome. Currently, consideration of HLA-DRB3/4/5, -DQA1, and -DPA1 for donor selection is hampered by the very low numbers of donors with available genotyping information in the registries. To overcome this limitation, we extended our genotyping profile for newly registered donors by including HLA-DRB3/4/5, -DQA1, and -DPA1. This reflects the recommendation of the current NMDP matching guidelines to use these genotypes for selection among multiple similar donors. Here, we focus on the implementation of these loci in our high-throughput NGS-workflow.