X-ray CT system and method of processing medical images are provided that enable combining of images with reduced effect of the differences in coordinates of the pixels in the overlapped areas of a plurality of constituent images. The X-ray CT system comprises a processor and a synthesizer. Based on coordinates of a first pixel in a first image that the image generator has generated about a first three-dimensional region of the subject and coordinates of a second pixel in a second image generated about a second three-dimensional region of the subject, the processor combines the first pixel with the second pixel on a one-for-one basis within a predetermined range in the rostrocaudal direction. The synthesizer generates a third pixel relative to the first pixel and the second pixel constituting the combination by the processor and to generate a third image that includes the third pixel.
