The structural change of a In-111-labelled azobenzene derivative was examined using the interference effect of electron-capture X-rays emitted by nuclear transformations in radioactive atoms. Interference fringes were generated between the direct monochromatic emission from the radioactive atoms and the emission totally reflected by the substrate surface. The site of a radioactive atom can be determined by analysing the measured interference fringes, because the period of these fringes depends on the position of the radioactive atoms relative to the substrate surface.