A powder sample of pure H 3 LiIr 2 O 6 was synthesized from α-Li 2 IrO 3 powder by a soft chemical replacement of Li + with H + . The crystal structure of H 3 LiIr 2 O 6 consists of sheets of edge sharing LiO 6 -and IrO 6 -octahedra forming a honeycomb network with layers stacked in a monoclinic distorted HCrO 2 type pattern. Heavy stacking faulting of the sheets is indicated by anisotropic peak broadening in the X-ray powder diffraction (XRPD) pattern. The ideal, faultless crystal structure was obtained by a Rietveld refinement of the laboratory XRPD pattern while using the LiIr 2 O 6 3− -layers of α-Li 2 IrO 3 as a starting model. The low radial distances of the PDF function, derived from synchrotron XRPD data, as constraints to stabilize the structural refinement. DIFFaX-simulations, structural considerations, high radial distances of the PDF function and a Rietveld compatible global optimization of a supercell were employed to derive a suitable faulting model and to refine the microstructure using the experimental data. We assumed that the overall stacking pattern of the layers in the structure of H 3 LiIr 2 O 6 is governed by interlayer O-H⋯O contacts.From the constitution of the layers, different stacking patterns with similar amounts of strong O-H⋯O contacts are considered. Random transitions among these stacking patterns can occur as faults in the crystal structure of H 3 LiIr 2 O 6 , which quantitatively describe the observed XRPD.