Electron diffraction offers advantages over X-ray based methods for crystal structure determination as it can be applied to sub-micron sized crystallites, and picogram quantities of material. With molecular organic species, however, crystal structure determination with electron diffraction is hindered by rapid crystal deterioration in the electron beam, limiting the amount of diffraction data that can be collected, and by the effect of dynamical scattering on reflection intensities. While automated electron diffraction tomography provides one possible solution, in this paper we demonstrate an alternative approach where a set of putative crystal structures of the compound of interest is generated using crystal structure prediction methods, and electron diffraction is used to determine which of these putative structures is in agreement with the available electron diffraction data. This approach enables the advantages of electron diffraction to be exploited, while avoiding the need to obtain large amounts of diffraction data or accurate reflection intensities. We demonstrate the methodology using the pharmaceutical compounds paracetamol, scyllo-inositol and theophylline.