A Confocal Acoustic Holography Microscope (CAHM) has been designed, simulated and partially verified experimentally to take holograms for non-invasive, three-dimensional measurements of a specimen's refractive indices from one view point. The designed and simulated prototype CAHM used a frequency of 2.25 MHz and measured sound speed changes of 16 m/s, temperature changes of 5°C and had a spatial resolution of 660 μm. With future improvements utilizing the latest technologies such as two-dimensional array detectors, Micro-Electro-Mechanical Systems (MEMS), and acoustic lenses, resolutions of 1 m/s, 0.5°C, and 150 μm are expected. The CAHM is expected to have many useful applications, including non-invasive mass and heat transfer measurements in fluids and materials and as a medical diagnostic tool to non-intrusively visualize compositions and temperatures within the human body.