The van der Waals layered magnet α−RuCl3 offers tantalizing prospects for the realization of Majorana quasiparticles. Efforts to understand this are, however, hampered by inconsistent magnetic and thermal transport properties likely coming from the formation of structural disorder during crystal growth, postgrowth processing, or upon cooling through the first order structural transition. Here, we investigate structural disorder in α−RuCl3 using x-ray diffuse scattering and three-dimensional difference pair distribution function analysis. We develop a quantitative model that describes disorder in α−RuCl3 in terms of rotational twinning and intermixing of the high- and low-temperature structural layer stacking. This disorder may be important to consider when investigating the detailed magnetic and electronic properties of this widely studied material.