The structure of metakaolin (calcined kaolinite clay; a common SCM used as a blending agent in many concretes as well as in geopolymer synthesis) has been a source of controversy for more than 50 years, with its disordered ("X-ray amorphous") layered structure resisting traditional crystallographic analysis. Total scattering analysis using both high-energy synchrotron X-rays and neutrons from a spallation source, in combination with density functional theory, has finally given insight into the details of this complex layered structure. An iterative methodology involving both neutron total scattering data and density functional theory (DFT) computations has shown the ability to generate a metakaolin structural model which is both experimentally and thermodynamically plausible. Furthermore, the process of kaolinite dehydroxylation has been simulated directly using density functional modelling, which provides insight into the mechanism of this transformation from crystalline to disordered, and the means by which the strained, reactive alumina sites in metakaolin are formed. These sites are seen to be predominantly 4-coordinated, with some sites that are strained 5-coordinated and a small number of 3-coordinated alumina sites; these identifications are supported by X-ray absorption near edge spectroscopy (XANES), although the results conflict with the current understanding of the system according to nuclear magnetic resonance (NMR) spectroscopy. We will provide discussion of the factors - experimental and samplerelated - which may contribute to this apparent discrepancy.