An endoscope apparatus includes: a light source apparatus that emits light in a wavelength band including a first wavelength band for exciting a first fluorescent substance and a second wavelength band an image pickup section that picks up an image of first fluorescence emitted when the first fluorescent substance is excited and an image of second fluorescence emitted when a second fluorescent substance provided on a treatment instrument is excited, to generate a fluorescence image an information storing section that stores shape information including information on a shape of the second fluorescent substance and an operation section that performs an operation to estimate an actual size of a region in which the first fluorescence is generated, based on a scaling factor calculated based on the shape information and a size of a draw region of the second fluorescence, and a size of a draw region of the first fluorescence.
