An image processing system according to an embodiment includes a first aligning unit, an output unit, a second aligning unit, and a display unit. The first aligning unit aligns first three-dimensional medical image data with second three-dimensional medical image data. The output unit outputs, as output data, data obtained by adding alignment information to the first three-dimensional medical image data and to the second three-dimensional medical image data or synthetic data obtained by aligning and synthesizing the first three-dimensional medical image data with the second three-dimensional medical image data. The second aligning unit receives the output data and aligns the second three-dimensional medical image data with one or a plurality of pieces of X-ray image data. The display unit displays image data obtained by aligning the first three-dimensional medical image data with X-ray image data based on an alignment result.
