A system for generating a three-dimensional image of the compressed breast 40 of a subject includes an x-ray mammography unit 24 for generating x-ray mammography data, a mechanical scanner 20 including an x-ray mammography compression paddle assembly 22, a control and motion system 26, 28 for driving the mechanical scanner 20 and for sensing the control and motion system's position, an ultrasound probe 32 for generating ultrasound image data in spatial registration with the x-ray mammography unit 24, and a computer 38 for generating from the ultrasound image data and the x-ray mammography data the three-dimensional ultrasound image. A method of examining a breast of a subject includes contacting an anterior surface of the breast with a compression paddle, applying pressure to the anterior surface of the breast with the compression paddle to compress it to reduce the thickness of the breast tissue, passing an ultrasound beam having a frequency greater than 3 MHz, perferrably about 5 MHZ or more, through the paddle and the compressed breast tissue, receiving echoes from the compressed breast tissue through the compression paddle, and converting the echoes into breast examination data.