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This paper is to present theoretical and experimental vibration analysis of fluid dynamic bearing (FDB) spindles with rotating-shaft design. In the theoretical analysis, a mathematical model is developed to predict half-speed whirls, rocking modes, frequency response functions (FRF), and transient responses. In the experimental studies, a FDB spindle with rotating-shaft design carrying four identical disks is tested. An impact hammer applies an impact force to the top disk in the out-of-plane direction and a capacitance probe measures the transverse vibration of the top disk. FRF and impulse response are obtained to verify the mathematical model.