In this paper we address the problem of recovering 3D non-rigid structure from a sequence of images taken with a stereo pair. We have extended existing non-rigid factorization algorithms to the stereo camera case and presented an algorithm to decompose the measurement matrix into the motion of the left and right cameras and the 3D shape, represented as a linear combination of basis-shapes. The added constraints in the stereo camera case are that both cameras are viewing the same structure and that the relative orientation between both cameras is fixed. Our focus in this paper is on the recovery of flexible 3D shape rather than on the correspondence problem. We propose a method to compute reliable 3D models of deformable structure from stereo images. Our experiments with real data show that improved reconstructions can be achieved using this method. The algorithm includes a non-linear optimization step that minimizes image reprojection error and imposes the correct structure to the moti...