Expression of MMP-9 mRNA, a type IV collagenase gene product, was followed during embryonic development of the mouse brain using in situ hybridization. Murine embryos from 7.5 to 15 days after fertilization were sectioned and evaluated for MMP-9 expression. During early development, from day 7.5 to day 9, no signal was detected in the cells of the neuroepithelium or in cells of the cephalic mesenchyme of the neural tube. At day 11, gene expression was localized to the Rathke's pouch and the germinal zone of the primitive ventricular system. At day 13, but most notably at day 15, high levels of MMP-9 were expressed by progenitor cells in close association with the development of structures, such as the hypophysis, the choroid plexus, the ganglion cell layer of the retina and the uveal tract. High MMP-9 mRNA levels were also associated with dense cellular aggregates destined to form the highly vascular grey matter of the brain. The presence of MMP-9 mRNA was confirmed using a ribonuclease protection assay. A 105 kDa gelatinase, consistent with the expected molecular mass for the murine MMP-9, was detected in embryonic brain extracts by substrate gel electrophoresis. To our knowledge, this is the first report on the localization of MMP-9 in developing neural tissues. Our results suggest that MMP-9 expression may have a previously unsuspected role in neural development.