Recently, Preimplantation Genetic Diagnosis (PGD) has been considered for several indications beyond its original purpose, not only to test embryos for a genetic disease, but also to select embryos for a non-disease trait, such as specific Human Leukocyte Antigen (HLA) haplotypes, related to immune compatibility with an existing affected child in need of an hematopoetic stem cell transplant. We report our experience on preimplantation HLA matching, describing strategies and overall outcome data of 60 cycles (54 for -thalassemia, 1 for Wiscott-Aldrich syndrome, 2 for Diamond-Blackfan anemia and 3 for Acute Lymphoid Leukaemia) from 45 couples overall, involving the testing of 486 embryos in combination with a genetic disease and 44 embryos for HLA matching only. An indirect single-cell HLA typing protocol based on a multiplex fluorescent polymerase chain reaction (PCR) of short tandem repeat (STR) markers scattered throughout the HLA complex was optimized. In 848/922 (92.0%) of blastomeres a successful amplification was achieved, obtaining a conclusive HLA matching diagnosis in 483/530 (91.1%) of the embryos tested. In total, 74 (15.3%) embryos revealed an HLA match with the affected siblings, 55 (11.4%) of which resulted unaffected and 46 (9.5%) have been transferred back to patients in 30 clinical cycles. Nine pregnancies were achieved, 5 healthy HLA matched children have been already delivered and cord blood stem cells were transplanted to 3 affected siblings, resulting in a successful hematopoietic reconstruction. These results represent one of the most extensive experience in the field and, complemented by other similar experiences, demonstrate that preimplantation HLA matching is a reliable alternative for the achievement of a successful treatment in children affected by severe congenital or acquired bone marrow disorder, in the absence of a compatible related donor.