Natural frequencies are used to identify the joint stiffness of a shaft-bearing system, where the shaft is assumed as a Rayleigh beam and the bearing as a linear spring. The eigenvalues for the case of uniform circular shaft are derived in a rigorous manner in terms of nondimensionalized parameters for the location of bearngs, bearing stiffness, and slenderness of the shaft. Then, sensitivities of the eigenvalues are calculated with respect to the stiffness ratio of shaft and bearing and the bearing location. Based upon these sensitivity charts, an iterative procedure is proposed to identify the bearing stiffness in an optimum sense. The step by step procedure is illustrated through a case study for a simple shaft-bearing system, where the stiffness of a set of ball bearings is successfully identified.