Considerable endeavors have been devoted to the synthesis of biocompatible scaffolds with tunable new structures and improved bioactivities. Within the field of bioceramics, silica-based ordered porous materials are receiving increasing attention by the biomaterials scientific community because silica is the main constituent of many biocompatible porous scaffold materials. In addition, dietary silicon plays an important role in bone formation and is markedly present in active calcification sites, stimulating the expression of genes involved in bone and cartilage formation and concurrently, inducing osteogenic differentiation and cell mineralization. More importantly, silicabased scaffolds hold their capability to host different guest molecules, representing a new generation of structurally unique materials. This chapter collects and discusses the current advances in silica-based scaffolds. The synthetic methods of tailoring scaffolding chemical composition and architecture are highlighted.