Sparc is a secreted calcium-binding glycoprotein that regulates mineralization of bone tissues in mammals. In other vertebrates, its function remains largely unclear. Here, we describe the isolation, genomic organization and expression of the sparc gene in the teleost Medaka (Oryzias latipes), an established vertebrate model for developmental studies. During earliest stages of Medaka embryogenesis, sparc is expressed in the sclerotome compartment of the somites that gives rise to precursor cells of the axial skeleton. Importantly, in this area its expression precedes that of twist-1, which is a crucial regulator of osteoblast formation. Dynamic expression is also found in the floor plate of the neural tube and the notochord. Both structures are passed by migrating skeletal precursors shortly before they differentiate and form the vertebrae. In general, sparc is expressed before the formation and mineralization of bone elements and expression of bone markers like collagen type 1a in the fins and axial skeleton of Medaka embryos. It is also expressed in several non-skeletal tissues of embryos and adult fish, suggesting possible other functions not related to bone mineralization. Taken together, the Medaka sparc gene represents an excellent marker for early sclerotome development. Its restricted and highly dynamic expression suggests a novel function during migration of sclerotome cells and their differentiation into early vertebrae. This marker thus allows the analysis of early skeletal development and formation of extracellular bone matrix in this vertebrate model.