Early events in kidney organogenesis involve reciprocal interactions between the ureteric bud and the metanephric mesenchyme, which lead to remodeling of the extracellular matrix. This remodeling involves matrix metalloproteases (MMPs), but the specific roles of individual MMPs in kidney development are not completely understood. Here, we analyzed MMP9-deficient mice at the first step of kidney development and found that MMP9 deficiency delayed embryonic kidney maturation and increased apoptosis ex vivo by 2.5-fold. These early defects resulted in a 30% decrease in nephron number, a 20% decrease in adult kidney weight, and altered kidney function and morphology at 12 mo. The membrane form of stem cell factor (SCF) increased, whereas the activated form of the SCF receptor, c-kit, decreased in MMP9-deficient embryonic kidneys. In organotypic culture, MMP9-deficient kidneys failed to secrete SCF, and addition of recombinant SCF partially rescued both apoptosis and the branching defect. In conclusion, these data show that MMP9 protects mesenchymal cells from apoptosis during kidney development and stimulates ureteric bud branching morphogenesis, most likely by releasing the soluble form of SCF, suggesting that normal renal development requires MMP9. The developing kidney is the product of reciprocal inductive interactions between the ureteric bud and its surrounding mesenchyme. These interactions are associated with the expression of extracellular matrix (ECM) components that play a crucial role in the establishment of cell polarity and epithelial phenotype of the mesenchyme and in the branching morphogenesis of the ureteric bud. 1 The role of ECM in branching morphogenesis was already pointed out 40 yr ago by Grobstein and Cohen, 2 who showed that collagenase inhibited embryonic salivary gland branching.Among the different families of proteases, special attention has been given to matrix metalloproteases (MMPs) and their inhibitors, the tissue inhibitors of metalloproteases (TIMPs). MMP2 and MMP9, which both belong to the type IV collagenase subfamily, are expressed early in the metanephros. 3 We first showed in an organotypic culture model that MMP9, but not MMP2, is required for ureteric bud branching at 11 d, the first step of metanephric development in the mouse. 3 However, MMP2 and its receptor MT1-MMP are involved 2 d later, at 13 d of mouse embryonic development. 4 In the rat, TIMP2, a MMP2 inhibitor, also inhibits branching morphogenesis at 13 d (corresponding to 12 embryonic d in the mouse). 5 In vitro studies using isolated ureteric buds grown in ECM gels confirmed the role of MMPs because ureteric bud