Improved experimental and clinical experiences resulted in continuously increasing numbers of allogeneic stem cell transplantation (SCT) during the past years. Nevertheless, severe immunologic side effects remain major risk factors. It is well known that disparities in major histocompatibility complex (MHC) genes and antigens play a dominant role in the induction of cellular immune responses, clinically manifested as graft versus host diseases (GVHD) or graft failures. In contrast, blood group differences, e.g. ABO incompatibilities, are often not considered as significant risk factors although severe clinical complications have been described after blood group-discrepant allogeneic SCT. Major ABO-incompatible SCT may lead to delayed cell engraftment and pure red cell aplasia. In contrast, minor ABO blood group incompatibilities are caused by administration of donor antibodies or by donor plasma cells leading to a passenger lymphocyte syndrome. Furthermore, several therapeutic methods such as T-cell depletion of stem cell transplants or treatment with cyclosporine without methotrexate are known as risk factors to develop immune hemolysis. Finally, it was recently demonstrated that other red blood cell antibodies such as anti-Kell inhibit the clonogenicity of erythrocyte and megakaryocyte progenitor cells and may therefore influence the engraftment after allogeneic SCT. Therefore, it is desirable for specialists in transfusion medicine to know the relevance of blood group antibodies in allogeneic SCT in order to perform diagnostic and/or therapeutic procedures. This article reflects the main immunologic and clinical risk factors in allogeneic SCT caused by blood group differences and corresponding antibodies.