A fluorescence microscope apparatus (1, 101, 102) comprising: a light source (2, 21, 22) that radiates excitation light onto a specimen; an objective optical system that collects fluorescence generated at the specimen due to the irradiation with the excitation light; an image capturing portion that captures the fluorescence collected by the objective optical system; a focal-position controller that causes the image capturing portion to capture images of the specimen at a plurality of focal positions by moving the focal position of the objective optical system in the optical axis direction of the objective optical system; an exposure-level controller that causes the image capturing portion to capture the fluorescence multiple times at the individual focal positions with differing exposure levels; and an image combining portion that generates combined images by combining the plurality of fluorescence images acquired by the image capturing portion at the each focal position in accordance with the control by the focal-position controller and the exposure-level controller; characterized in that the fluorescence microscope apparatus (1, 101, 102) further comprises: a smoothed-luminance calculating portion that calculates a representative luminance from the individual combined images generated by the image combining portion and that calculates a smoothed luminance for the individual combined images by smoothing the calculated representative luminance in the optical axis direction; a luminance correcting portion that generates corrected images by correcting the luminance of the individual combined images on the basis of differences between the smoothed luminance and the representative luminance calculated by the smoothed-luminance calculating portion; and a three-dimensional image generating portion that generates a three-dimensional image of the specimen from the plurality of corrected images generated by the luminance correcting portion. a light source (2, 21, 22) that radiates excitation light onto a specimen; an objective optical system that collects fluorescence generated at the specimen due to the irradiation with the excitation light; an image capturing portion that captures the fluorescence collected by the objective optical system; a focal-position controller that causes the image capturing portion to capture images of the specimen at a plurality of focal positions by moving the focal position of the objective optical system in the optical axis direction of the objective optical system; an exposure-level controller that causes the image capturing portion to capture the fluorescence multiple times at the individual focal positions with differing exposure levels; and an image combining portion that generates combined images by combining the plurality of fluorescence images acquired by the image capturing portion at the each focal position in accordance with the control by the focal-position controller and the exposure-level controller; characterized in that the fluorescence microscope apparatus (1, 101, 102) further comprises: a smoothed-luminance calculating portion that calculates a representative luminance from the individual combined images generated by the image combining portion and that calculates a smoothed luminance for the individual combined images by smoothing the calculated representative luminance in the optical axis direction; a luminance correcting portion that generates corrected images by correcting the luminance of the individual combined images on the basis of differences between the smoothed luminance and the representative luminance calculated by the smoothed-luminance calculating portion; and a three-dimensional image generating portion that generates a three-dimensional image of the specimen from the plurality of corrected images generated by the luminance correcting portion. a smoothed-luminance calculating portion that calculates a representative luminance from the individual combined images generated by the image combining portion and that calculates a smoothed luminance for the individual combined images by smoothing the calculated representative luminance in the optical axis direction; a luminance correcting portion that generates corrected images by correcting the luminance of the individual combined images on the basis of differences between the smoothed luminance and the representative luminance calculated by the smoothed-luminance calculating portion; and a three-dimensional image generating portion that generates a three-dimensional image of the specimen from the plurality of corrected images generated by the luminance correcting portion.