To investigate the role of matrix metalloproteinases (MMPs) during gastrointestinal tract development, the expression of gelatinases (MMP-2 and MMP-9) was investigated during fetal rat colon morphogenesis. Fetal rat colons were separated into epithelial and mesenchymal fractions without cross contamination using a chelating agent and a dissecting microscope. Gelatinase activity measured using fluorescently labeled gelatin was higher in the mesenchymal than in the epithelial fraction; the developmental profile revealed that, in both fractions, gelatinase activity was enhanced during colon morphogenesis. During colonic gland formation, there was prominent MMP-2 activity, elevated MMP-2 mRNA expression, and an increase in the level of the active form of MMP-2 in the mesenchymal fraction. The mRNA expression of the tissue inhibitor of metalloproteinase 2 corresponded with an elevation in the level of the active form of MMP-2; the mRNA expression of the cell surface activator of MMP-2, membrane type matrix metalloproteinase 1, did not increase significantly. MMP-9 activity was low; only the pro-form was observed in the epithelial fraction at the end of fetal life. These results suggest that, during colon morphogenesis, MMP activity is under strict spatio-temporal control, and that the activity of MMP-2, which is regulated at both the transcriptional and proteolytic activation levels, is very much involved in rat colon morphogenesis.