Diamond has unique physical, thermal, electrical, and optical properties with respect to other minerals and related synthetic compounds that make it extremely valuable from an economic and industrial perspective. Natural diamond that forms in the upper mantle, transition zone, and lower mantle may encapsulate mantle minerals during growth and protect them from physical breakdown and chemical alteration upon ascent of the diamond to the surface via kimberlite eruption. Such mineral inclusions serve as the only direct means to study the deep Earth and provide critical information about the pressure, temperature, and redox conditions and the chemical and isotopic composition of the mantle. Natural diamonds show a wide range of ages and thus allow one to reconstruct the history of large-scale Earth processes, such as the formation and amalgamation of Earth’s lithosphere, the onset and evolution of tectonic processes (e.g., Wilson cycles), and the recycling of C, H, and N between different primordial and crustal reservoirs. In this review, a detailed description of all types of imperfections (e.g., mineral and fluid inclusions and structural defects) and the methods by which such imperfections can be analyzed to elucidate aspects of Earth’s complex geologic history is given.