Considerable remodeling of the extracellular matrix as well as cellular migration takes place during embryogenesis. Since the metalloproteinase MMP‐9 is implicated in these functions in cancer cells, we studied the patterns of expression of MMP‐9 mRNA during the development of post‐implantation mouse embryos. MMP‐9 mRNA was detected using the ribonuclease protection assay in poly A + RNA from 13 to 17 day embryos, but not at 11 days. In order to localize these transcripts, in situ hybridization was performed on sections of murine embryos from 7.5 to 15 days of gestation. At the time of implantation, MMP‐9 mRNA was localized to the invading trophoblast cells. Strong signals were also seen in the yolk sac. No signal for MMP‐9 mRNA was seen by in situ hybridization in the embryo until day 11 when detectable reaction was seen in the central nervous system. By day 15 strong signals were seen in the liver, in the developing bronchial epithelium of the lungs and in the primordial alveoli, in the epithelium of the thyroid gland, in the thymus, in the endochondrial plates of the bone, and in neural cells. The liver from day 15 embryos contained gelatinase activity at 105 kDa consistent with MMP‐9. Thus, MMP‐9 expression appears to be expressed in specific organs in a precise temporal sequence during development. © 1995 wiley‐Liss, Inc.