The temporal stability of a Carreau fluid flowing down an inclined porous substrate is considered. A reduced model is derived under the assumption of small permeability which decouples the flow in the liquid layer from the filtration flow in the porous medium and incorporates the effect of the porous medium by means of an effective slip condition at the liquid-solid interface. The slip coefficient in the effective slip condition is a function of the structure, permeability of the porous medium and the rheology of the fluid saturating the porous medium. The effects of shear-thinning rheology and permeability of the substrate on the stability of the film flow system are investigated. This problem gives rise to a generalized eigenvalue formulation which is solved through two approaches. The problem is solved analytically for long waves in the limiting cases of weakly and strongly non-Newtonian behaviors (power-law limit). A numerical investigation is carried out in the general case. The results are shown to agree well for the weakly non-Newtonian limit. Further, the power-law model and the Carreau model agree on a wide range of shear-thinning parameter values for a thin film over a rigid substrate. However, when considering a porous medium, this trend is not observed. The Carreau model gives valid results for the entire range of shear-thinning parameter values for a film over a rigid/porous substrate. The novelty of the present investigation lies in the inclusion of both the effects of bottom permeability and shear-thinning rheology. Both permeability and shear-thinning rheology have a destabilizing effect on the film flow system. The numerical results indicate the correlation between the effects due to shear-thinning properties and permeability. An energy balance analysis performed on the perturbation fields shows that destabilization induced by both shear-thinning and permeability is linked to the viscous shear work rate on the free surface. © 2011 Elsevier Ltd.