This paper deals with the stiffness analysis of multibody systems using the Matrix Structural Analysis—MSA. This methodology allows us to obtain the stiffness matrix of the structure from the stiffness properties of each element. First the MSA method is described and its application is detailed using an L-structure in order to make easy its understanding. Numerical and experimental results obtained for the L-structure and a 6-RSS parallel manipulator, follow to prove the validity of the methodology.