The accurate calculation of the viscosity eta as function of the shear rate (gamma )over dot from capillary viscometry is still a matter of debate in the literature. In fact, this problem involves the inversion of an integral equation, which leads to multiple solutions due to the unavoidable noise present in the experimental data. The purpose of this work is to develop an efftcient procedure to determine the viscosity function from experimental data of capillary flow without presenting the difficulties inherent in other methods discussed previously in the literature. The system identification procedure is used here to estimate the parameters of a viscosity model, which is appropriately selected for the fluid under study through preliminary calculations involving the apparent shear rate - shear stress data. Once the model is chosen by satisfying criteria for the fit goodness and its parameters are evaluated, a smooth and continuous function eta((gamma )over dot) is obtained in the range of experimental shear rates. The procedure proposed is also applicable to fluids in shear flow that present two Newtonian plateaus, as it is typically found in macromolecular dilute solutions. The mean value theorem of continuous functions is used to reduce significantly the computational time.