The coxsackie and adenovirus receptor (CAR) is a member of the immunoglobulin superfamily and a component of vertebrate tight junctions. CAR protein is widely expressed in fish and mammals in organs of epithelial origin suggesting possible functions in epithelial biology. In order to gain insight into its function, we knocked the CAR gene down in zebrafish using antisense morpholinos. We identified a requirement for CAR in the terminal differentiation of glomerular podocytes and pronephric tubular epithelia. Podocytes differentiate in CAR morphants but are not able to elaborate a regularly patterned architecture of foot processes. In the tubules, CAR was required for the apposition of plasma membranes from adjacent epithelial cells but did not appear to be necessary for the formation of tight junctions. Additionally, tubular epithelia lacking CAR were not able to elaborate apical brush border microvilli. These results establish a requirement for CAR in the terminal differentiation of renal glomerular and tubular cell types.