In many cases, idealized crystal structure models cannot rationalize the actual properties of intermetallic compounds. For a realistic approach in materials research, microstructures and defects need to be taken into account. In case of clathrate compounds, particularly the intrinsic framework vacancies (denoted as Zintl defects) demand consideration. Consequently, clathrate research produces evidence that modern‐day structure chemistry involves the utilization of advanced X‐ray diffraction methods combined with elaborated bulk phase analyses, the investigation of phase relations, and the study of mutual interrelations in the triangle chemical bonding–structure–properties. Herein, we review some fundamental contributions to the specific defect chemistry of intermetallic clathrates.