Transmission electron microscopic (TEM) studies have not been reported in bone marrow (BM) biopsies of patients with myelodysplastic syndromes (MDS) owing to failure to overcome the technical impediment of maintaining ultrastructural detail in decalcified tissue. Using a modified technique to physically separate pieces of bone from marrow tissue under a dissecting microscope, and embedding the material directly for TEM, ultrastructural studies were performed in 15 MDS patients and four normal BM biopsies. Biopsy tissue was also used to initiate long-term in vitro cultures and 12-week plates were sacrificed for TEM analysis. Features noted in freshly obtained decorticated tissue included an excessive apoptosis in both haematopoietic and stromal cells, ringed sideroblasts with iron-laden mitochondria and highly active, enormously increased phagocytosis. In addition, type IV nuclear inclusion body variants (NIB-v) and confronting cylindrical cisternae (CCC) were readily identified in up to 40% of stromal cells in vivo, providing an important footprint of a possible infectious agent in the pathology of MDS. Cultured stromal cells did not show excessive apoptosis and only 2-4% fibroblasts showed the presence of NIB-v or CCC, underscoring the artificial nature of ex vivo systems. We conclude that ultrastructure studies using decorticated tissue can be a powerful tool to investigate the biology and aetiology of a variety of haematopoietic disorders as it enables the direct examination of BM biopsies with their intimate stromal parenchymal cell associations preserved intact.