The growing demand for high-quality transportation fuels requires their cost-effective production by hydrodesulfurization of crude oils using heterogeneous catalysts. To study the three-dimensional (3D) structure of such a commercial, sulfided Ni-Mo/gamma-Al2O3 catalyst, electron tomography was applied. The MoS2 particles form an interconnected complex structure within the mesopores of the alumina support. Spatial organization, morphology, and orientation of the MoS2 particles in the pores were resolved with sufficient accuracy to display the 6-A-spaced MoS2 crystal planes. The proximity of the MoS2 edge planes and more loosely interacting MoS2 basal planes to the alumina support showed the presence of pores smaller than 3 nm, which was confirmed by physisorption experiments. The actual shape of the MoS2 particles cannot be described by simple models as derived from studies on model catalysts. Electron tomography is a unique tool to study the actual 3D structure of complex industrial catalysts with sub-nanometer resolution.