Layered double hydroxides (LDH) are a broad group of widely studied materials. The layered character of those materials and their high flexibility for accommodating different metals and anions make them technologically interesting. The general formula for the LDH compound is [M1-xIIMxIII(OH)2][An-]x/n·mH2O, where MII is a divalent metal cation which can be substituted by MIII trivalent cation, and An- is a charge compensating anion located between positively charged layers. In this paper we present a comprehensive study on possible structural disorder in LDH. We show how X-ray powder diffraction (XRPD) can be used to reveal important features of the LDH crystal structure such as stacking faults, random interlayer shifts, anion-molecule orientation, crystal water content, distribution of interlayer distances, and also LDH slab thickness. All calculations were performed using the Discus package, which gives a better flexibility in defining stacking fault sequences, simulating and refining XRPD patterns, relative to DIFFaX, DIFFaX+, and FAULTS. Finally, we show how the modeling can be applied to two LDH samples: Ni0.67Cr0.33(OH)2(CO3)0.16·mH2O (3D structure) and Mg0.67Al0.33(OH)2(NO3)0.33 (2D layered structure).