Measurement method of material parameters for uniaxial anisotropic medium from the S-parameters which show the reflection and transmission characteristics of the electromagnetic waves in the rectangular waveguide from the target sample has been presented in this paper. At first, by using two rectangular waveguides with different size of aperture, the measurement setup has been shown, and also the formulas to estimate the uniaxial anisotropic material parameters have been derived. The validity of this measurement method is verified by the electromagnetic simulation for anisotropic materials.