Deer antler regeneration is a uniquely intense and complex process, which involves chondrogenic and intramembranous ossification. Cell differentiation in the developing antler of red deer, Cervus elaphus, was characterized with extracellular matrix markers. Expression of the four matrilin genes was monitored by immunohistochemistry and in situ hybridization and compared to cartilage markers collagen II and cartilage link protein, the bone component collagen I, and the endothelial basement membrane constituent laminin. The mesenchyme layer at the very tip of the velvet antler was enriched in link protein, indicative of the role of hyaluronan in apical morphogenesis. Matrilin-2, formerly described as a component of hard and soft connective tissue matrices, was identified here also as a marker of cells with high differentiation potential: it is expressed predominantly by mesenchyme cells, prechondrocytes and preosteoblasts. In addition to matrilin-3, documented as a component of the bony extracellular matrix, expression of the other three matrilin genes was observed in osteoprogenitor cells and osteoblasts. A layer of presumed osteoprogenitor cells, which surrounded the perivascular channels, expressed all four matrilins and collagen I. As a consequence, all four matrilins, including matrilin-1, previously detected in the skeleton only in cartilage, were found associated to collagen I-rich structures in a thin layer bordering the columns of hypertrophic chondrocytes. Cells with similar morphology and expression pattern were identified in the periosteum. Altogether all cell types of the chondrogenic and osteogenic lineage that expressed the four matrilins were in a separate study [Faucheux, C., Nicholls, B.M., Allen, S., Danks, J.A, Horton, M.A., Price, J.S., 2004. Recapitulation of the parathyroid hormone-related peptide-Indian hedgehog pathway in the regenerating deer antler. Dev. Dyn. 231, 88-97] positive for parathyroid hormone-related peptide and its receptor.