Scube genes encode a small group of secreted plasma membrane-associated proteins characterised by a N-terminal signal peptide sequence, multiple EGF domains, a N-linked glycosylated spacer region and a C-terminal CUB region. Here we describe expression of the mouse Scube3 gene during early embryonic development. Transcripts were initially localised to neurectoderm of the developing embryo, in the ventral rhombencephalon and caudal neuropore. However, as development progressed, strong expression was detected in ectodermal, endodermal and mesodermal tissues. In particular, the neural tube, branchial arches and fronto-nasal region, the dermomyotome of differentiating somites and the limb buds. Scube3 also demonstrated a highly restricted and specific expression domain in the developing tooth and hair follicle. At later stages, expression was also localised to cartilaginous primordia of the skeleton and regions of intramembranous bone formation in the developing craniofacial region. In addition, Scube3 transcripts were also found in the developing kidney.