A system align point clouds obtained by sensors of a vehicle using kinematic iterative closest point with integrated motions estimates. The system receives lidar scans from a lidar mounted on the vehicle. The system derives point clouds from the lidar scan data. The system iteratively determines velocity parameters that minimize an aggregate measure of distance between corresponding points of the plurality of pairs of points. The system iteratively improves the velocity parameters. The system uses the velocity parameters for various purposes including for building high definition maps used for navigating the vehicle.