A structure diagnosis apparatus 1 for diagnosing a state of a structure in which there is a small change in the natural frequency includes: a natural vibration extraction unit 2 configured to acquire, from a plurality of sensors 21 that a structure is provided with 20, vibration information indicating vibration generated in the structure 20, and extracting natural vibration using the vibration information; a spectral shape extraction unit 3 configured to extract spectral shape information indicating a shape of a spectrum using the natural vibration; an index calculation unit 4 for calculating an index indicating a relationship between the spectral shape information and reference spectral shape information that is a preset reference; and a state estimation unit 5 for estimating the state of the structure based on the index.