The formation of fullerene crystals represents a major degradation pathway of polymer/fullerene bulk-heterojunction thin films that inexorably deteriorates their photovoltaic performance. Currently no tools exist that reveal the origin of fullerene crystal formation vertically through the film. Here, we show that electron tomography can be used to study nucleation and growth of fullerene crystals. A model bulk-heterojunction blend based on a thiophene-quinoxaline copolymer and a fullerene derivative is examined after controlled annealing above the glass transition temperature. We image a number of fullerene nanocrystals, ranging in size from 70 to 400 nanometers, and observe that their center is located close to the free-surface of spin-coated films. The results show that the nucleation of fullerene crystals predominately occurs in the upper part of the films. Moreover, electron tomography reveals that the nucleation is preceded by more pronounced phase separation of the blend components.