Morphogenesis of epithelial cells involves processes by which kidney shape and function are regulated. The lack of in vitro models that are sustainable for longer time periods and emulating complex intercellular interactions of the kidney have limited understanding about epithelial tissue morphogenesis and its aberrations in diseases such as autosomal dominant polycystic kidney disease (ADPKD). A sustainable three-dimensional (3D) coculture system for normal and diseased kidney tissues is reported here. Tubule- and ADPKD cyst-derived cells were cultured in extracellular matrix molecules infused into 3D porous silk scaffolds, and these cultures were subsequently extended into a perfusion bioreactor. The results indicated collagen-matrigel-mediated morphogenesis for both (normal and disease) cell types and also supported coculturing with fibroblasts. The structural and functional features of the kidney-like tissue structures were validated based on the distribution of E-cadherin, N-cadherin, Na+ K+ ATPase pump, and cellular uptake of the organic anion (6-carboxy fluorescein). Further, the structures were sustained for longer time periods using a perfusion bioreactor to demonstrate the potential utility of this 3D in vitro coculture system for ADPKD research, other epithelial tissue systems, and for in vitro drug screening.