PROBLEM TO BE SOLVED: To provide a sample structure analysis method capable of accurately identifying a grain boundaries and regions which are hard to identify in a contrast comparison between images, and to provide a transmission electron microscope and to provide a program. ! SOLUTION: A sample structure analysis method includes the steps of: generating a beam to irradiate a plurality of observation regions on a sample and acquiring a plurality of diffraction images from the beam transmitted through the sample; and comparing the plurality of acquired diffraction images one another, and determining difference between the observation regions from a comparison result or identifying grain boundaries of a crystal composing the sample. ! COPYRIGHT: (C)2015,JPO&INPIT