It is provided a technique capable of noninvasively and quantitatively evaluating the state of cultured three-dimensional cell-based structure. A method of evaluating a three-dimensional cell-based structure according to the present invention comprises: performing tomography of the cultured three-dimensional cell-based structure (step S103)； generating stereoscopic data indicating the three-dimensional shape of the three-dimensional cell-based structure based on image data acquired by the tomography (step S104)； and counting the number of structures isolated from each other in the three-dimensional cell-based structure based on the stereoscopic data (step S105).
