Haematopoietic stem cell transplantation (HSCT) is a curative treatment of many hematological disorders. However, although significant advances have been made in donor-recipient matching or conditioning regimens, HSCT is associated with a risk of post transplant complications. Those include generation of toxic lesions, graft-versus-host-disease (GvHD) and viral reactivations. Recent studies have shown the association between polymorphic features of non-HLA encoding genes and the incidence and severity of post-transplant complications in the recipients of allogeneic HSCT, implying that the donorrecipient genotyping, extended for cytokine loci, may be of prognostic value for the transplantation outcome. Thus, the pre-transplant analysis of the patients genetic predisposition may be considered as important factor allowing the classification of the transplant recipients as less or more susceptible for developing toxic lesions, severe and/or fatal acute GvHD or viral reactivation. This review focuses on the relationship between the polymorphic patterns of tumor necrosis factor (TNF)-α and TNF-β, IFN-γ, interleukin (IL)-6, IL-10 and heat shock protein (HSP)70-hom encoding genes and the manifestation of post-transplant complications, acute and chronic GvHD, generation of toxic lesions, viral reactivations and mortality.