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To satisfy the low loss requirement of magnetically suspended rotors, such as energy-storage flywheel, a novel radial permanent-magnet biased magnetic bearing (RPMB) with low rotating loss due to low flux fluctuation frequency in rotor core called homopolar 2-pole RPMB was proposed. A rotating loss separation method was also proposed, which was based on the Bertotti loss model, but without measurement of model's coefficients. In virtue of the flywheel equipped with the homopolar 2-pole RPMB and the 4-pole RPMB successively, two types of bearings' rotating loss could be separated from flywheel run-down loss. The experimental results showed that the classic loss accounts for the majority of each type bearing's rotating loss at 30 000 rpm, and the rotating loss of the homopolar 2-pole RPMB was slightly more than half of the homopolar 4-pole RPMB. It could be inferred that the effect on the loss reduction of homopolar 2-pole RPMB would be more significant, for high speed or large power applications.