Stereo visual odometry and dense scene reconstruction depend critically on accurate calibration of the extrinsic (relative) stereo camera poses. We present an algorithm for continuous, online stereo extrinsic re-calibration operating only on sparse stereo correspondences on a per-frame basis. We obtain the 5 degree of freedom extrinsic pose for each frame, with a fixed baseline, making it possible to model time-dependent variations. The initial extrinsic estimates are found by minimizing epipolar errors, and are refined via a Kalman Filter (KF). Observation covariances are derived from the Cr´amer-Rao lower bound of the solution uncertainty. The algorithm operates at frame rate with unoptimized Matlab code with over 1000 correspondences per frame. We validate its performance using a variety of real stereo datasets and simulations.