The improvement of the sol-gel processes has provided a new generation of silica-based ordered mesoporous materials (OMM) for biomedical applications and bone tissue engineering. These materials, indeed, have been suggested as matrices for sustained drug release, showing that both small and large molecular drugs can be entrapped and released from the mesopores through several different processes. Many emerging biotechnologies can benefit from these OMM-based drug delivery systems. For instance, bone tissue engineering is a growing area directed towards the design of materials able to improve the bone regeneration capacity by recovering both its structure and function. In this area, controlled drug delivery from biocompatible and bioactive mesoporous materials with sufficient mechanical strength could favor the cellular growth and bone regeneration. Ordered mesoporous silica (OMS) present a high drug loading capacity and a controlled sustained release which could be helpful for this purpose, however their poor bioactive behaviour and mechanical properties drove to the development of new bioactive systems. On one hand mesoporous bioactive glasses (MBGs) have been extensively investigated, on the other hand the combination of OMS and bioactive macroporous scaffolds has been proposed in order to obtain hierarchical systems for bone substitution.