Complex structures are usually assembled from several substructures with joints connecting them together. These joints have significant effects on the dynamic behavior of the assembled structure and must be accurately modeled. In structural analysis, these joints are often simplified by assuming ideal boundary conditions. However, the dynamic behavior predicted on the basis of the simplified model may have significant errors. This has prompted the researchers to include the effect of joint stiffness in the structural model and to estimate the stiffness parameters using inverse dynamics. In the present work, structural joints have been modeled as a pair of translational and rotational springs and frequency equation of the overall system has been developed using sub-structure synthesis. It is shown that using first few natural frequencies of the system, one can obtain a set of over-determined system of equations involving the unknown stiffness parameters. Method of multi-linear regression is then applied to obtain the best estimate of the unknown stiffness parameters. The estimation procedure has been developed for a two parameter joint stiffness matrix.