The nanocrystalline αII-phase of the industrially produced organic pigment quinacridone was studied by 3D electron diffraction of its crystals with a thickness of only 10 nm. The diffraction data showed strong diffuse scattering along one direction indicating severe stacking disorder. The average crystal structure was obtained from electron diffraction data using direct methods. In αII-quinacridone, the molecules are connected by a pair of hydrogen bonds thereby forming molecular chains, which are stacked, resulting in the formation of layers. The layers exhibit a stacking disorder with a mixture of herringbone and parallel arrangements, which explains the diffuse scattering. The crystal structure was confirmed by dispersion-corrected DFT calculations.