Chiral crystals can be exploited for applications in enantioselective separation and catalysis. However, the study of chirality at the atomic level in a sub-micrometre-sized crystal is difficult due to the lack of adequate characterization methods. Herein, we present two efficient and practical methods of characterization that are based on electron crystallography. These methods are successfully applied to reveal the handedness of a chiral, zeolite nanocrystal. The handedness is identified through either a comparison of two high-resolution transmission electron microscope images, taken from the same nanocrystal but along different zone axes by tilting it around its screw axis, or the intensity asymmetry of a Bijvoet pair of reflections in a single precession electron-diffraction pattern. These two approaches provide new ways to determine the handedness of small, chiral crystals.