Structure-function relationships in mineralized tissues, such as bone and teeth, depend upon the chemical interactions of the interfaces between cells, proteins, organic matrix, and mineral (calcium phosphate). Development of in vitro models that more accurately model mineralization systems in vivo will assist in understanding medical conditions as well as inform biomimetic materials development. Understanding the heirachical structures in mineralized tissues relies on the chemical control of crystal nucleation and growth at the interfaces. Studies presented in this thesis provide additional in vitro tools for studying in vivo systems by controlling for interface chemistry, mineralization environment, and experimental setup for elucidating the effect of interfaces in biomineralization. Covalently bound surface chemistry - oxide, methyl, carboxylate, 2-aminoethyl dihydrogen phosphate, osteopontin, and bovine serum albumin (BSA) - on porous silicon substrates has a distinct affect on surface mineral nucleation and morphology. The morphology and coverage resulting from suspending the differed from those reported in literature. This method has potential for selectively examining the effects of covalently bound protein conformations and segments, more closely mimicking the conformation constraints at interfaces in biological systems. Hydrogel-based double diffusion system (DDS) has the potential to allow for the simultaneous in vitro study of cell-mineral-matrix interactions in a 3-D environment, the 'holy-grail' of mineralization studies. Successful hydroxyapatite mineralization was demonstrated at both room temperature and incubator conditions using a custom build polycarbonate DDS with polydimethylsiloxane membranes for gas permeability, minimal polyethyleneimine coating for gel adhesion, and cell culture compatible Agarose. This system provides researchers with a new tool for combining cell, mineral, and matrix in a 3-D environment for understanding the complexity of cell-mineral-matrix interactions. Understanding how proteins interact with surface chemistry as well as their structural changes and coverage, provides important clues towards biology's ability to exert control over biomineralization. Analysis of the monolayer-protein interface via infrared spectroscopy demonstrated that the protein conformation increases in disorder upon adsorption to the surface based on amide peak positions and amounts of adsorbed protein varied as a function of chemistry. Work in this thesis provides tools and information towards developing in vitro systems that elucidate complex interactions in mineralized tissues.