Using endoscopic video, it is possible to perform 3D reconstruction of the anatomy using the well known epipolar constraint between matched feature points. Through this constraint, it is possible to recover the translation and rotation between camera positions and thus reconstruct the 3D anatomy by triangulation. However, these motion estimates are not stable for small camera motions. In this work, we propose a covariance estimation scheme to select pairs of frames which give rise to stable motion estimates, i.e. minimal variance with respect to pixel match error. We parameterize the essential matrix using a minimal 5 parameter representation and estimate motion covariance based upon the estimated feature match variance. The proposed algorithm is applied to endoscopic video sequences recorded in porcine sinus passages in order to extract stable motion estimates.