We present two methodologies for the design of robust fault isolation observer for linear uncertain systems. The proposed fault isolation observer is robust to structural uncertainties by producing disturbance decoupled residuals. The first method uses a direct eigenstructure assignment scheme to accomplish a diagonal transfer function between the faults and the residuals. The second method is carried out through transformation of the linear system under consideration into its special coordinate basis (SCB) form. Once the system is in SCB form, we propose a disturbance decoupled fault detection observer (DDFDO) which is combined either with Beard–Jones detection filter (BJDF) theory, or input estimation results. This will lead to the final proposed robust fault detection filter. Finally, two numerical examples are given in order to illustrate the validity and effectiveness of the proposed fault detection and isolation (FDI) strategy. Copyright © 2000 John Wiley & Sons, Ltd.