The understanding of fundamental phenomena involved in tissue engineering and regenerative medicine is continuously growing and leads to the demand for three-dimensional (3D) models that better represent tissue architecture and direct cells into the proper lineage for specific tissue repair. Porous 3D scaffolds are used in tissue engineering as templates to allow cell attachment and tissue formation. Scaffold design plays a central role in guiding cells to synthesize and maintain new tissues. While a number of techniques have been developed and are now in use for high-throughput screening of combinatorial factors involved in biotechnology in two-dimensions, high-throughput screening in 3D is still in its infancy. There is a broad interest in developing similar techniques to assess which variables are critical in designing 3D scaffolds to achieve proper and lasting tissue regeneration. We describe, herein, a number of studies adopting smart scaffold design and in vitro and in vivo analysis as the basis for 3D model systems for evaluating combinatorial factors influencing cell differentiation and tissue formation.