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Fault detection and isolation (FDI) in rotor systems often faces the problem that the system dynamics is dependent on the rotor rotary frequency because of the gyroscopic effect. In unbalance excited rotor systems, the continuously distributed unbalances are hard to be determined or estimated accurately. The unbalance forces as disturbances make fault detection more complicated. The aim of this paper is to develop linear time invariant (LTI) FDI methods (i.e., with constant parameters) for rotor systems under consideration of gyroscopic effect and disturbances. Two approaches to describe the gyroscopic effect, that is, as unknown inputs and as model uncertainties, are investigated. Based on these two approaches, FDI methods are developed and the results are compared regarding the resulting FDI performances. Results are obtained by the application in a rotor test rig. Restrictions for the application of these methods are discussed.