© 2015 The Franklin Institute. Published by Elsevier Ltd. All rights reserved. This paper presents a functional observer based fault detection method. The fault detection is achieved using a functional observer based fault indicator that asymptotically converges to a fault indicator that can be derived based on the nominal system. The asymptotic value of the proposed fault indicator is independent of the functional observer parameters and also the convergence rate of the fault indicator can be altered by choosing appropriate functional observer parameters. The advantage of using this new method is that the observed system is not necessarily needed to be observable; therefore, the proposed fault detection technique is also applicable for systems where state observers cannot be designed; moreover, the functional observer fault detection scheme is always of reduced order in comparison to a state observer based scheme.