Composite materials with unique architectures are ubiquitous in nature, e.g., marine shells, sponge spicules, bones, and dentine. These structured organic-inorganic systems are generated through self-assembly of organic matter (usually proteins or lipids) into scaffolds, onto which the inorganic component is deposited in organized hierarchical structures of sizes spanning several orders of magnitude. The development of bio-inspired materials is possible through the design of synthetic bottom-up self-assembly methods. Knowledge of the structure is required in order to assess the efficiency of their design and evaluate their properties. This chapter reviews the main methods used for structure determination of natural and synthetic inorganic biomaterials, namely, X-ray diffraction and scattering and electron diffraction and microscopy (TEM, SEM), as well as the AFM and CSLM microscopy methods. Moreover, spectroscopic (IR, NMR, and Raman) and thermal methods are presented. Examples of biomimetic synthetic materials are used to show the contribution of single or multiple techniques in the elucidation of their structure.