Self-renewing organs in adult mammals are composed of numerous tissue-specific functional units, such as intestinal crypts/villi or hair follicles, which all involve stem cell (SC) niches. Analogous tissue units in haematopoietic systems, however, have remained elusive. We design here a step-by-step protocol for in situ mapping, purification, enumeration and structural-functional analysis of the haematopoietic tissue unit, termed haematon. Longitudinal bisection of mouse femur and careful, limited dispersion of bone marrow (BM) parenchyma reveals compact, node-like haematons at discreet capillary loops along the diaphysis and spongy metaphysis. Recovery and fractionation of the whole BM in a bulk cell suspension, haematon units and endosteal layer provides a reproducible tool for quantitative and topographical analysis of putative SC niches in defined tissue compartments. We show examples how to characterize haematons in native state or following long-term culture using laser-scanning confocal microscopy, flow cytometry, clonal bioassays and videomicroscopy. osteoblasts 25 , vascular endothelium 26,27 , reticular stroma cells 28 , mesenchymal stem cells 29 and nonmyelinated Schwann cells 30 as critical niche forming cells operating via a plethora of effector signaling factors (see for Review 22,31,32). These accumulating complementary and sometimes concurrent data reflect the complexity of the HSC niche's function and reinforce the emerging consensus accordingly the HSC niche is a dynamic, multicellular construct 32. Concordant information obtained in solid organs documents that (a) tissue units are quantifiable (hair and whisker papillae, taste buds, nephrons 33), (b) SC niches are basic, constitutive elements of individualized tissue units 2,3,4,8 , and (c) functional niches are multi-cellular constructs which always involve several interacting cell types 6,8. Based on these universal characteristics of tissue units we have postulated previously that HSCs and several interacting stroma cells constitute, together, the functional core of BM. We have, indeed, identified such native tissue units in the human and mouse BM 34-38 but theirs in situ topography, cellular and molecular composition and their relationship with the HSC niche have not been clearly documented. We have now improved our previously described techniques, adapted pertinent methods and thus elaborated a robust protocol for the reproducible purification and structural-functional analysis of stem cell/stroma units in mammalian blood-forming tissues. Diverse applications of the protocol The protocol, optimized for mouse blood-forming organs includes whole body perfusion, recovery of the whole BM parenchyma and surrounding endosteum by micro-dissection, biophysical separation in three principal cell compartments and comparative structural, functional and quantitative analyses. The protocol can be routinely applied for: (i) topographical investigation of critical marrow stroma cells and haematopoietic stem/progenitor cells, (ii) purification of putative...