A structure of interest (T) is irradiated with radiation for example in the x-ray or EUV waveband, and scattered radiation is detected by a detector (19, 274, 908, 1012). A processor (PU) calculates a property such as linewidth (CD) or overlay (OV), for example by simulating (S16) interaction of radiation with a structure and comparing (S17) the simulated interaction with the detected radiation. The method is modified (S14a, S15a, S19a) to take account of changes in the structure which are caused by the inspection radiation. These changes may be for example shrinkage of the material, or changes in its optical characteristics. The changes may be caused by inspection radiation in the current observation or in a previous observation.