The scattering cross-section of atoms in biological macromolecules for both elastically and inelastically scattered electrons is ∼100,000 times larger than that for x-ray. Therefore, much smaller (<1 μm) and thinner (<0.01 μm) protein crystals than those used for x-ray crystallography can be used to analyze the molecular structures by electron crystallography. But, inelastic scattering is a serious problem. We examined electron diffraction data from thin three-dimensional (3-D) crystals (600-750 Å thick) and two-dimensional (2-D) crystals (∼60 Å thick), both at 93 K, with an energy filtering electron microscope operated at an accelerating voltage of 200 kV. Removal of inelastically scattered electrons significantly improved intensity data statistics and RFriedel factor in every resolution range up to 3-Å resolution. The effect of energy filtering was more prominent for thicker crystals but was significant even for thin crystals. These filtered data sets showed better intensity statistics even in comparison with data sets collected at 4 K and an accelerating voltage of 300 kV without energy filtering. Thus, the energy filter will be an effective and important tool in the structure analysis of thin 3-D and 2-D crystals, particularly when data are collected at high tilt angle.