The initiation and detonation properties of explosives are often empirically correlated to density, surface area, and particle size. Although these correlations are sometimes used successfully to predict the performance of bulk samples, the data are spatially averaged, which unfortunately muddles information critical to understanding fundamental processes. Density and surface area are essentially an indirect measure of porosity, which is arguably a more appropriate metric in many applications. We report the direct characterization of porosity in polycrystalline molecular crystal explosives by focused ion beam nanotomography, a technique that is typically reserved for robust materials such as ceramics and metals. The resulting three-dimensional microstructural data are incredibly rich, promising a substantial advance in our ability to unravel the processes governing initiation and detonation of molecular crystal explosives. In a larger context, this work demonstrates that focused ion beam nanotomography may be successfully extended to the investigation of nanoscale porosity in other molecular crystal or polymer materials.