The primary function of the kidneys is to filter waste from blood, and the kidney glomeruli are the major site for filtration. The glomerulus is a blood filtration barrier with low resistance to small molecules, but is relatively impermeable to macromolecules. Each glomerulus consists of a blood capillaries network with endothelial cells on a basement membrane, the other side of which is lined with specialized epithelial cells known as podocytes. The integrity and function of the glomerular filtration barrier is critical for kidney function, and disruption of this barrier correlates with kidney disease progression, and eventually kidney failure. Current research models for kidney disease include animal models, 2D, and 3D kidney epithelial cell cultures. However, animal models suffer from high cost and are too complex for studying detailed cellular interactions, while existing in vitro models lack the architecture and components to fully reproduce in vivo conditions. We propose a 3D microphysiological system that recapitulates the endothelial-epithelial interface found in the kidney glomerulus. We have developed a method to form independent microscale channels within a collagen I substrate, separated by a very thin layer of collagen. Collagen I is a native matrix protein that supports cell growth, invasion, and exchange of cellular signals. Primary endothelial and epithelial cells has been seeded into the channels to form closed lumina, whose overlaps form the endothelial-epithelial interface. However, culture conditions remain to be optimized to support both types of cells. Structure, morphology, and function of the interface are monitored by confocal microscopy, biochemical assays, and electron microscopy. When fully developed and validated, this culture system can be used to study the transport properties and injury responses of glomerular filtration. It can also provide a platform for drug screening to identify compounds toxic to the kidney, or therapeutic compounds for kidney diseases.