In one embodiment, an MRI apparatus includes a memory storing a predetermined program and processing circuitry. The processing circuitry is configured, by executing the predetermined program, to generate a first image having a first phase affected by susceptibility, generate a second image having a second phase affected by both of the susceptibility and flow, and distinguish difference in susceptibility or flow for a pixel of a third image by using the first phase and the second phase or by using a value calculated from the first phase and a value calculated from the first phase, the third image having regions which are substantially same in contrast.
