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This work evaluated system identification-based approaches for estimating stretch reflex contributions to muscle dynamics. Skeletal muscle resists externally imposed stretches via both intrinsic stiffness properties of the muscle and reflexively mediated changes in muscle activation. To separately estimate these intrinsic and reflex components, system identification approaches must make several assumptions. The authors examined the impact of making specific structural assumptions about the intrinsic and reflex systems on the system identification accuracy. In particular, they compared an approach that made specific parametric assumptions about the reflex and intrinsic subsystems to another that assumed more general nonparametric subsystems. A simulation-based approach was used so that the "true" characters of the intrinsic and reflex systems mere known; the identification methods were judged on their abilities to retrieve these known system properties. Identification algorithms were tested on three experimentally based models describing the stretch reflex system. Results indicated that the assumed form of the intrinsic and reflex systems had a significant impact on the stiffness separation accuracy. In general, the algorithm incorporating nonparametric subsystems was more robust than the fully parametric algorithm because it had a more general structure and because it provided a better indication of the appropriateness of the assumed structure.