Movement simulations consist of models involving skeletal structure, muscle paths, musculotendon actuation, muscle excitation-contraction coupling, and a motor task goal (Pandy, 2001). Development of an accurate inverse dynamic model of the skeletal structure is a significant first step toward creating a predictive patient-specific forward dynamic model to perform movement simulations. The precision of dynamic analyses is fundamentally associated with the accuracy of kinematic model parameters such as segment lengths, joint positions, and joint orientations (Andriacchi and Strickland, 1985; Challis and Kerwin, 1996; Cappozzo et al., 1975; Davis, 1992; Holden and Stanhope, 1998; Holden and Stanhope, 2000; Stagni et al., 2000). Understandably, a model constructed of rigid links within a multi-link chain and simple mechanical approximations of joints will not precisely match the human anatomy and kinematics. The model should provide the best possible agreement to experimental motion data within the bounds of the joint models selected (Sommer and Miller, 1980). Benefits of Two-Level Optimization This thesis presents a nested (or two-level) system identification optimization approach to determine patient-specific joint parameters that best fit a three-dimensional (3D), 18 degree-of-freedom (DOF) lower-body model to an individual's movement data. The two-level technique combines the advantages of using optimization to determine both the position of model segments from marker data and the anatomical joint axes linking adjacent segments. By formulating a two-level objective function to minimize marker coordinate errors, the resulting optimum model more accurately represents experimental marker data (or a specific patient and his or her motion) when compared to a nominal model defined by joint axes prediction methods.