Abstract: Systems and methods are provided for serial, high-throughput acquisition of electron diffraction patterns from nanocrystals. Nanocrystals dispersed on a TEM grid are automatically identified from an overview image that is obtained, for example, using a dark field detector in scanning mode. Diffraction patterns are subsequently obtained from a plurality of crystals identified in the overview image by sequentially moving (e.g. scanning) the electron nanobeam relative to the crystals and collecting diffraction images using a fast electron camera. In some example embodiments, this sequence may be repeated for different tilt angles, where registration among overview images obtained at the different tilt angles is employed to position the electron nanobeam for the different tilt angles (e.g. before the sample stage is moved to interrogate a different sample region). The present methods may be automated, thereby facilitating unsupervised acquisition of arbitrarily large data sets.