Minor histocompatibility antigens (mHags) play a major role in graft-versus-host disease (GvHD) and graft-versus-leukaemia (GvL) effect following human leucocyte antigen (HLA)-matched hematopoietic stem cell transplantation (HSCT). These antigens are defined as immunogenic peptides derived from polymorphic proteins and can be recognized by allogeneic cytotoxic T cells (CTLs) in the context of HLA molecules. The tissue distribution of mHags and HLA molecules influences the clinical outcome of T-cell responses to these antigens. Differential T-cell recognition of mHags specifically expressed in hematopoietic cells, including malignant cells from the recipient, may result in a beneficial GvL effect without detrimental GvHD. Furthermore, T-cell responses against proteins solely expressed in hematopoietic cell lineages from which the malignancy is derived may be appropriate mediators of GvL reactivity without GvHD induction. mHags with hematopoiesis-restricted expression may therefore serve as primary targets of the T-cell-mediated GvL/graft-versus-tumour (GvT) effect following HLA-identical HSCT. This paper reviews the recent findings on methods for identification of mHags specifically functioning as GvL/GvT targets and outlines perspectives for the development of novel strategies for mHag-based immunotherapy.