A sensitivity distribution generating apparatus configured to generate sensitivity distribution data of a coil for receiving magnetic resonance signals from an imaging region including a first substance and a second substance different in resonant frequency is provided. The sensitivity distribution generating apparatus includes a reference image data generating unit configured to generate reference image data in which a region of the first substance is suppressed and a region of the second substance is emphasized, based on data obtained by executing a separation sequence for separating the first substance and the second substance from each other, and an estimating unit configured to estimate a sensitivity of the coil in the region of the first substance, based on a signal value of the region of the second substance in the reference image data.