A method and system generates and compares fingerprints for videos in a video library. The video fingerprints provide a compact representation of the spatial and sequential characteristics of the video that can be used to quickly and efficiently identify video content. Because the fingerprints are based on spatial and sequential characteristics rather than exact bit sequences, visual content of videos can be effectively compared even when there are small differences between the videos in compression factors, source resolutions, start and stop times, frame rates, and so on. Comparison of video fingerprints can be used, for example, to search for and remove copyright protected videos from a video library. Further, duplicate videos can be detected and discarded in order to preserve storage space.