To acquire a medical image with high quality to be hardly affected by the movement of a subject.

The modality 11 of a medical image generation apparatus images the medical image, so as to analyze the frequency of the imaged medical image and to determine whether the medical image is the image with the movement equal to or more than reference. When the movement is determined to be equal to or more than the reference, the modality abandons the image, acquires the image of the same imaging position of the subject again, re-evaluates the image, and acquires the imaged image without the movement. When two-dimensional tomographic images are superposed so as to form a three-dimensional image, the modality 11 obtains coincidence between the i-th two-dimensional tomographic image and the (i-1)-th two-dimensional tomographic image, while shifting the i-th (i is the natural number of two or more) two-dimensional tomographic image, specifies a shift amount with the maximum coincidence, corrects the position of the i-th two-dimensional tomographic image by a specified shift amount, repeats processing to superpose the (i-1)-th two-dimensional tomographic image, and then, forms the three-dimensional medical image.