Tolerance analysis method for natural frequencies of multi-body systems having a equilibrium position is suggested in this paper. To perform the tolerance analysis, the Monte-Carlo Method is conventionally employed. However, the Monte-Carlo Method has some weakness; spending too much time for analysis and having a low accuracy and hard to converge in the dynamical unstable area. To resolve these problems, a tolerance analysis method is suggested in this paper. Sensitivity equations of natural frequencies are derived at the equilibrium position. By employing the sensitivity information of mass, damping and stiffness matrices, the sensitivity of natural frequencies can be calculated.