Silk fibroin is an important polymer for scaffold designs, forming biocompatible and mechanically robust biomaterials for bone, cartilage, and ligament tissue engineering. In the present work, 3D biomaterial matrices were fabricated from silk fibroin with controlled pore diameter and pore interconnectivity, and utilized to engineer bone starting from human mesenchymal stem cells (hMSC). Osteogenic differentiation of hMSC seeded on these scaffolds resulted in extensive mineralization, alkaline phosphatase activity, and the formation of interconnected trabecular- or cortical-like mineralized networks as a function of the scaffold design utilized; allowing mineralized features of the tissue engineered bone to be dictated by the scaffold features used initially in the cell culture process. This approach to scaffold predictors of tissue structure expands the window of applications for silk fibroin-based biomaterials into the realm of directing the formation of complex tissue architecture. As a result of slow degradation inherent to silk fibroin, scaffolds preserved their initial morphology and provided a stable template during the mineralization phase of stem cells progressing through osteogenic differentiation and new extracellular matrix formation. The slow degradation feature also facilitated transport throughout the 3D scaffolds to foster improved homogeneity of new tissue, avoiding regions with decreased cellular density. The ability to direct bone morphology via scaffold design suggests new options in the use of biodegradable scaffolds to control in vitro engineered bone tissue outcomes. © Mary Ann Liebert, Inc.