Understanding the movement of tumors caused by respiratory motion is very important for conformal radiatherapy. However, respiratory motion is very difficult to study by conventional x-ray CT imaging since object motion causes inconsistent projection views, leading to artifacts in reconstructed images. We propose to estimate the parameters of a nonrigid, free breathing motion model from a set of projection views of the thorax that are acquired using a slowly rotating cone-beam CT scanner. This approach involves deforming a motion-free reference thorax volume according to the estimated parameters and comparing its projections to the corresponding measured projection views. The parameters are optimized by minimizing a regularized squared error cost function. Simulation results with a fan-beam geometry show good agreement between the estimated motion and the true motion, which supports the potential of this approach for estimating four-dimensional (three-dimensional spatial + temporal) respiratory motion.