This work concerns the tracking problem of uncertain Takagi-Sugeno fuzzy continuous systems with unmeasurable premise variables and affected by unknown inputs. The aim is to synthesize a fault tolerant controller (FTC) ensuring trajectory tracking of a desired reference model. To emit the original plant system, a norm bounded parametric uncertainty is employed in building the T-S model. The control scheme is based on a fuzzy observer to estimate both faults and faulty system states; a proportional integer (PI) observer to estimate constant faults is then adopted. Using descriptor redundancy property and L-2 optimization to attenuate the unknown inputs effect, a solution is proposed in terms of bilinear matrix inequalities (BMIs). The performances of the proposed approach are pointed out by accentuating on a model of wastewater treatment plant (WWTP) through numerical results. (C) 2012 Elsevier Ltd. All rights reserved.