To develop structure-performance relationships for important catalysts, a detailed characterization of their morphology is essential. Using electron tomography, we determined in three dimensions the structure of Pt/zeolite Y bifunctional catalysts. Optimum experimental conditions enabled for the first time high-resolution 3D imaging of Pt particles as small as 1 nm located inside zeolite micropores. Semiautomated image analysis of 3D reconstructions provided an efficient study of numbers, size distributions, and interparticle distances of thousands of Pt particles within individual zeolite crystals. Upon extending this approach to a number of zeolite crystals of one batch of Pt/zeolite Y catalyst, heterogeneities were revealed. The Pt loading, an important parameter for catalyst performance, varied between zeolite crystals up to a factor of 35. This discovery calls for re-evaluation of catalyst preparation methods and suggests potential for lowering the nominal loading with noble metals.