At its primary level (nm scale) bone is a nanocomposite consisting of a mineral (hydroxyapatite) phase which gives bone its strength and an organic (type I collagen) phase giving bone its fracture toughness. Hydroxyapatite, (HAP) Ca10(PO4)6(OH)2, is the most abundant mineral in the human body. Bone tissue has a complex hierarchical structure spanning multiple length scales (cm to nm). Characterization of mineral composition in biomineralized tissues such as bone at their primary level, is very challenging and requires instrumentation with nanometer-scale spatial resolution. Transmission electron microscopy (TEM) combines high spatial resolution with visual correlation of diffraction and elemental-composition data. Electron energy-loss spectroscopy (EELS) is a sensitive technique used to probe electronic structure at the molecular level. TEM-based EELS is the only available technique that can provide information about the chemical and coordination environment of minerals with nm scale spatial resolution. Prior studies in our group has developed a method to create biomimetic HAP using biomineralization routes inside the clay galleries of montmorillonite clay modified with amino acids (in-situ HAPclay). Incorporation of in-situ HAPclay into polymer scaffolds and seeding with human mesenchymal stem cells has enabled the cells towards differentiation into osteoblastic lineages without differentiating media. Because of the importance of these materials for bioengineering applications, TEM-EELS was used to evaluate differences and similarities among HAP, biomimetic in-situ HAPclay, modified MMT clay, and β-tricalcium phosphate. Osteogenesis imperfecta (OI), also known as brittle bone disease, is an inheritable disease characterized by increased bone fragility, low bone mass, and bone deformity caused primarily by mutation in collagen type I genes and is expressed as changes in structure and mechanics at the macrostructural level of bone. Therefore the mineralization of HAP in OI bone and the molecular basis of OI bone disease makes this an interesting system for molecular-level investigations. Small changes in the valence band and outer electronic structures of the diseased bone have been revealed through EELS. These small changes observed in the electron energy-loss spectra of the OI bone appear to play important biological roles towards development of the disease.