A comparative characterization of crystal structure, morphology, sizes, and orientation in Ca phosphate precipitation from aqueous solutions, the mineral phase in bones, and mineral deposits on cardiac valves has been performed by high-resolution transmission electron microscopy to model possible mechanisms of Ca loss by bones. Physiological changes occurring in organisms can lead to deep perturbations of the natural calcium phosphate supersaturation and its local distribution, which in turn influences the phase composition, morphology, and organization of the mineral phase. Formation of crystals with larger size or of two distinct phases instead of the single hydroxyapatite one can result in the deterioration of the Ca balance in bone and tissue destruction as well as the possible misorientation (or spread of orientation) between HAP crystals newly formed in the bone.