ABSTRACT The use of Bayesian techniques in Finite Element Model (FEM) updating has recently increased. These techniques have the ability to quantify and characterize the uncertainties of dynamic structures. In order to update a FEM, the Bayesian formulation requires the evaluation of the posterior distribution function. For large systems, this functions is either difficult (or not available) to solve in an analytical way. In such cases using sampling techniques can provide good approximations of the Bayesian posterior distribution function. The Hybrid Monte Carlo (HMC) method is a powerful sampling method for solving higher-dimensional complex problems. The HMC uses the molecular dynamics (MD) as a global Monte Carlo (MC) move to reach areas of high probability. However, the acceptance rate of HMC is sensitive to the system size as well as the time step used to evaluate MD trajectory. To overcome this, we propose the use of the Separable Shadow hybrid Monte Carlo (S2HMC) method. This method generates samples from a separable shadow Hamiltonian. The accuracy and the efficiency of this sampling method is tested on the updating of a GARTEUR SM-AG19 structure