BackgroundNew strategies to optimize donor selection for hematopoietic stem cell transplantation (HSCT) have mainly been evaluated in adults, but the disease spectrum requiring HSCT differs significantly in children and has consequences for the risk of complications, such as graft‐versus‐host disease (GvHD).ProceduresHere we evaluated whether HLA‐DPB1 and Predicted Indirectly ReCognizable HLA‐Epitope (PIRCHE) matching can improve donor selection and minimize risks specific for a pediatric cohort undergoing HSCT in Berlin between 2014 and 2016.ResultsThe percentage of HLA‐DPB1–mismatched HSCT in the pediatric cohort was in line with the general distribution among matched unrelated donor HSCT. Nonpermissive HLA‐DPB1 mismatches were not associated with a higher incidence of GvHD, but the incidence of relapse was higher in patients undergoing HSCT from HLA‐DPB1–matched transplantations. High PIRCHE‐I scores were associated with a significantly higher risk for developing GvHD in patients undergoing HSCT from nine of ten matched unrelated donors. This finding persisted after including HLA‐DPB1 into the PIRCHE analysis.ConclusionsImplementing PIRCHE typing in the donor selection process for HSCT in children could particularly benefit children with nonmalignant diseases and support further validation of PIRCHE‐based donor selection in a larger number of children treated at different sites.