Abstract Several techniques have been applied to analyze the pore size, pore shape and pore structure of MCM-41. In order to assess the significance of X-ray diffraction (XRD) data and transmission electron microscopy (TEM) images, we constructed a computer model (CERIUS2 of Molecular Simulations, San Diego, CA, 1996) of an amorphous silica with a unidimensional pore system and hexagonally shaped pores. From the simulation of TEM focus series and crystal thickness series of this model, it can be seen that the picture obtained strongly depends on imaging conditions. In addition, we used the model to simulate diffraction patterns of defect structures: destroying the hexagonal array of the pores or simulating a broader pore size distribution in the model structure, often has only a minor influence on the simulated diffraction patterns. Although these findings are not unexpected, it might be useful to keep the limitations of the methods used in mind, if conclusions concerning the structural properties of MCM-41 are drawn from XRD or TEM data alone.