Apoptosis of haemopoietic cells in the marrow of patients with myelodysplastic syndrome (MDS) has been suggested as a mechanism for peripheral cytopenias. We determined the expression of Fas (CD95), Fas‐Ligand (Fas‐L) and TNF‐α factors known to be involved in apoptosis, in the marrow of 44 patients with MDS and characterized their functional relevance in in vitro assays of haemopoiesis. Multidimensional flow cytometry revealed phenotypically aberrant blasts as defined by orthogonal light scatter and CD45 expression in the marrow of 24/44 patients. Among those blasts Fas expression was increased on CD34‐positive cells and on cells co‐expressing HLA‐DR. In addition, Fas‐L was expressed on some CD34+ cells of MDS patients but was never detected on CD34+ cells in normal marrow. Fas and Fas‐L mRNAs as well as mRNA for TNF‐α, known to increase Fas expression in normal marrow, were up‐regulated in patients with MDS. TNF‐α protein and sTNF‐R1 levels in marrow plasma were higher in MDS patients than in controls (P < 0.002 and <0.003, respectively). However, results were dependent upon disease category: TNF‐α levels were significantly higher in patients with refractory anaemia (RA) than in patients with RA with excess blasts (RAEB) or RAEB in transformation (RAEB‐T) (P = 0.043). Conversely, the proportion of Fas‐L‐positive cells was lowest in patients with RA (P = 0.037). In marrow cultures, Fas‐Ig, rhuTNFR:Fc or anti‐TNF‐α antibody, by blocking Fas or TNF mediated signals, respectively, significantly increased the numbers of haemopoietic colonies compared to untreated cells (P < 0.001, P < 0.003, P < 0.001, respectively). These results show significant dysregulation in the expression of TNF‐α, Fas and Fas‐L in the marrow from MDS patients. Altered expression of these molecules appears to be of functional relevance in the dysregulation of haemopoiesis in MDS and may be amenable to therapeutic interventions.