The bony biochemical environment is a complex system that permits and promotes cellular functions that lead to matrix production and ossification. In Part I of this review, we discussed the important actions of signaling molecules, including hormones, cytokines, and growth factors. Here, we review other constituents of the extracellular matrix, including minerals, fibrinous and nonfibrinous proteins, and enzymes such as the matrix metalloproteinases. We conclude with a discussion of the role of biochemical modulation in endogenous and exogenous tissue engineering.