Preimplantation Genetic Diagnosis (PGD) of single gene disorders, combined with HLA matching, has recently emerged as a tool for couples at risk of passing on a genetic disease to select embryos both free of the disease and of a compatible Human Leukocyte Antigen (HLA) tissue type with an existing affected child. Stem cells from the resulting baby’s umbilical cord blood could be used in the treatment of the affected sibling, that without stem cell transplant is likely to die. This approach is particularly valuable for -thalassemia or others similar life-threatening disorders requiring HLA compatible stem cell donor, in which molecular HLA identity between donors and recipients seems to provide the best chance for avoiding graft rejection and other serious complications of bone marrow transplantation. In this paper we describe an alternative strategy optimized for PGD of genetic disorders, requiring stem cells transplantation, combined with HLA matching. This procedure involves a minisequencing-based genotyping of HLA regions A, B, C, DRB combined with mutation analysis of the gene regions involved by mutation. Analysis of different polymorphic STR markers scattered throughout HLA complex was also included to increase accuracy of the analysis and to detect potential contaminations and crossing over occurrence between HLA genes. In this study, our aim was to optimize a flexible preimplatation HLA matching protocol appropriate for the analysis of a wide spectrum of possible HLA genotypes, precluding the design of case specific protocols each time. Clinical application of this strategy involved 16 cycles of HLA genotyping in combination with PGD for for -thalassemia, sickle cell anemia, and Wiskott-Aldrich syndrome. In addition, one cycle for preimplantation HLA matching without testing for a causative gene was performed for a leukaemia case. Using this assay 14 HLA compatible embryos resulted both free of the disease and HLA compatible with the affected child and was transferred back to patient, resulting in 4 clinical pregnancies. These results confirm once again the usefulness of preimplantation HLA matching as a part of PGD, providing a realistic option for couples desiring to have a HLA compatible child for the treatment of affected siblings.