Great variations exist in the practices of graft-versus-host disease prophylaxis for children undergoing allogeneic stem cell transplantation. It was the aim of the EBMT Working Party on Paediatric Diseases and the International Study Group of the BFM-Family, subcommittee bone marrow transplantation (IBFM-SG) to define standard recommendation for prevention of GVHD. Thus a survey was carried out among the local representatives of the EBMT WP and IBFM-SG members to define standards for GVHD prophylaxis basing on available literature data, discussion with colleagues and their own experience. Presently the majority of regimen for GVHD prophylaxis are centred on CsA and a short course of MTX with addition of some other immunosuppression (eg ATG or ALG) in patients with high risk for severe GVHD. The proposal defined different category of patients: patients with malignant disease who are either transplanted from HLA matched sibling donors or HLA mismatched family donors (or volunteer unrelated donors) and patients with non malignant disease who might not benefit from graft-versus-leukaemia effect having either an HLA matched sibling donor or an HLA mismatched family donor (or volunteer unrelated donor). Homogeneous GVHD prophylaxis for defined patient groups should provide better information to optimise strategies in reducing treatment related toxicity and incidence of relapse by increasing GVL effect.