What is disclosed is a system and method for compensating for motion induce artifacts in a physiological signal obtained from a video. In one embodiment, a video of a first and second region of interest of a subject being monitored for a desired physiological function is captured by a video device. The first region is an area of exposed skin wherein a desired signal corresponding to the physiological function can be registered. The second region is an area where movement is likely to induce motion artifacts into that signal. The video is processed to isolate pixels in the image frames associated with these regions. Pixels of the first region are processed to obtain a time-series signal. A physiological signal is extracted from the time-series signal. Pixels of the second region are analyzed to identify motion. The physiological signal is processed to compensate for the identified motion.