In this review paper a uniform matrix formalism enabling us to include the important defects of thin film systems into the formulae for their optical quantities is presented. The following defects are discussed: roughness of the boundaries; inhomogeneity represented by profiles of the refractive indices; transition interface layer and volume inhomogeneity. It is shown that this formalism is relatively very efficient. Thus fact is demonstrated using a theoretical example representing a complicated thin film system exhibiting defects.