Video alignment and calibration, which is needed for video quality measurement in full-reference mode, is performed continuously on the videos being measured to account for alignment parameters that may change over time. With this technique, the quality of video files and/or live video streams can be measured in full-reference mode in real-time. During video alignment, the temporal and spatial offsets, as well as any spatial, luminance or color transformations between the two videos are measured; during video calibration, the video frames are adjusted for these offsets and transformations so that the video quality can be measured correctly.