A rotordynamic analysis is performed with a centrifuge rotor-bearing system for the raing speed of 100,000 rpm. The system is composed of a centrifuge rotor(or simply the rotor), flexible shaft, motor rotor and shaft, and two support rolling element bearings of the motor shaft. Design goals are to achieve wide separation margins of critical speeds and favorable unbalance responses of the rotor at the associated critical speeds. The latter requirements are especially important as the system crosses multiple numbers of critical speeds and as the system may not have enough separaton margins around the rating speed. As the system adopts an extra-flexible shaft, it is shown that the rotor has satisfactory small unbalance responses over higher criticals while having an unsatisfactory large one at the first critical. To supress this a bumper ring or guide bearing needs to be installed at a suitable location of the flexible shaft. It is also shown that even with the flexible shaft the dynamics of the motor must be incoporated into the full system model to accurately identify the fourth critical speed, which is close to the rating speed, and higher ones. The analysis is based on the finite element method.