A three-dimensional medium-energy ion scattering (3D-MEIS) spectrometer has been developed for crystallographic structure analysis of materials. In 3D-MEIS, a pulsed He+ ion beam at 100keV is incident upon a sample and scattered (and/or recoiled) particles are detected by a three-dimensional detector. The three-dimensional detector used is a position-sensitive and time-resolving microchannel plate detector with two delay-line anodes intersecting at right angles. 3D-MEIS has been employed to analyze the structure of an Er silicide film on a Si(111) substrate. A blocking pattern based on the structure of the Er silicide was clearly observed. The results indicate that 3D-MEIS is effective for crystallographic structural analysis of materials.