A system and method of performing ultrasound modulated optical tomography. Ultrasound is delivered into a target voxel in an anatomical structure, and sample light is delivered into the anatomical structure, whereby a portion of the sample light passing through the target voxel is scattered by the biological tissue as signal light, and a portion of the sample light not passing through the target voxel is scattered by the anatomical structure as background light. The ultrasound and sample light are pulsed in synchrony, such that only the signal light is frequency shifted by the ultrasound. Multiple pulses of the sample light are delivered into the anatomical structure for each pulse of the ultrasound delivered into the target voxel. Reference light is combined with the signal light and background light to generate an interference light pattern, which is sequentially modulated to generate different interference light patterns, which are detected.
