A computer aided disease detection system and method for multiple organ systems. The method performs computer aided examination of digital medical images. A patient exam type of a digital medical image is determined. Based on the patient exam type, one or more of a plurality of knowledge based anatomical segmentation blocks are invoked, each block performing image segmentation for a single organ or organ system present in the image. Based on the patient exam type, for each successfully segmented organ or organ system, one or more of a plurality of knowledge based computer aided detection blocks are invoked, each block of which is designed to search for and locate potential disease foci in a particular organ or organ system.