A medical diagnosis assistance system comprising an image data storage part, a substance distribution information acquiring part, a display part; and a control part. The image data storage part is configured to store image data of a brain function image. The substance distribution information acquiring part is configured to detect the signal from within the brain of a subject and to acquire, based on the detected signal, substance distribution information indicating the distribution of the quantity of specified endogenous substances in each part of the brain. The control part is configured to control the display part to display the brain function image and the image information based on said acquired substance distribution information.