Pax2 has been identified as a key regulatory protein associated with renal developmental malformations. The purpose of this study was to determine whether Pax2 protein expression, and that of other proteins important for normal renal development, is abnormally distributed in the prenatal kidney of the Brachyrrhine ( Br) mouse that displays heritable renal hypoplasia. Embryonic 3H1 +/+ and Br/Br mice were collected between E11.0 and E18.0. Routine light microscopy and immunohistochemical analysis using antibodies to Pax2, E-cadherin, fibronectin, laminin, and Type IV collagen were applied to sequential tissue sections. E-cadherin stained consistently in the renal tubules of both normal and mutant animals. Whereas the initial expression of Pax2 corresponded between normal and mutant kidneys, it became progressively limited to the nephrogenic zone in +/+ animals, while distributing erratically in the Br/Br kidney. Fibronectin was not expressed in the normal nephrogenic zone but remained abundantly distributed throughout the Br/Br kidney. Luminin and Type IV collagen staining revealed a deficiency in renal vasculature formation in Br/Br kidneys. Results suggest that initial morphological differentiation occurs normally in the Br kidney but that subsequent nephric formation is associated with abnormal distribution of Pax2 and ECM proteins. (J Histochem Cytochem 49:1081–1097, 2001)