It has recently been shown that the model in experimental design can be expressed in terms of an orthonormal system. In this case, the model is expressed by using Fourier coefficients instead of the effect of each factor. As there is an abundance of software for calculating the Fourier transform, such a system allows for a straightforward implementation of the procedures for estimating the Fourier coefficients by using Fourier transform. However, Fourier coefficients themselves do not provide a direct representation of the effect of each factor, and the relation between the Fourier coefficients and the effect of each factor has not yet been clarified. In this paper, we present theorems of the relation between the Fourier coefficients and the effect of each factor. By using these theorems, the effect of each factor can be easily obtained from the computed Fourier coefficients. Therefore, with the aid of an orthonormal system, it is possible to easily implement the estimation procedures as well as to understand how each factor affects the response variable in the model.