Density functional modeling of the crystalline layered aluminosilicate mineral kaolinite is conducted, first to reconcile discrepancies in the literature regarding the exact geometry of the inner and inner surface hydroxyl groups, and second to investigate the performance of selected exchange-correlation functionals in providing accurate structural information. A detailed evaluation of published experimental and computational structures is given, highlighting disagreements in space groups, hydroxyl bond lengths, and bond angles. A major aim of this paper is to resolve these discrepancies through computations. Computed structures are compared via total energy calculations and validated against experimental structures by comparing computed neutron diffractograms, and a final assessment is performed using vibrational spectra from inelastic neutron scattering. The density functional modeling is carried out at a sufficiently high level of theory to provide accurate structure predictions while keeping computational requirements low enough to enable the use of the structures in large-scale calculations. It is found that the best functional to use for efficient density functional modeling of kaolinite using the DMol(3) software package is the BLYP functional. The computed structure for kaolinite at 0 K has C-1 symmetry, with the inner hydroxyl group angled slightly above the a,b plane and the inner surface hydroxyls aligned close to perpendicular to that plane.