High specific mechanical properties of composites are the reason for their use in various fields, e.g., the aerospace industry. Mechanical joints are still used in the aerospace industry to assembly large aircraft structures. The properties of laminate around the hole can be, however, weakened, compared to their nominal values as a result of a drilling process or cyclic loading. This paper aims at the classification and analysis of imperfections affecting mechanically fastened joints in a laminate structure. A method of modeling the hole vicinity, a gradient material model, as well as the numerical and experimental estimation of laminate deterioration in this area, were proposed and analyzed. Comparative analysis of numerical and experimental results based on displacements of the testing machine grip and the extensometer length confirmed the aforementioned results as consistent in linear ranges. Therefore, joint characteristics obtained based upon measurement of the grip displacement and the ratio of stiffness in linear ranges are sufficient to determine the parameters of a gradient material model. Some imperfections resulting from, e.g., asymmetry, were included in the gradient material model; thus, the obtained weakening of laminate properties in the hole vicinity can be overestimated. Therefore, further analyses of the gradient material model for laminate structures are necessary.