The physical and optical characteristics of a multilayered synthetic microstructure (MLSM) have a significant structural dependence. Knowledge of the structure and its correlation to physical properties is needed in order to control the fabrication of MLSMs to obtain desired properties. Important parameters for the description of the structure are the thickness of a repeating unit, the thickness ratio of composite materials within the repeating unit and the degree of interdiffusion and roughness at interfaces. The effects of these various structural parameters on the small-angle x-ray diffraction (XRD) pattern are investigated for a molybdenum-silicon MLSM. The angular positions of the Bragg peaks are sensitive to the thickness of the repeating unit (Mo/Si bilayer in this study), and the pattern of the subsidiary peaks in the low-order Bragg region has a strong dependence on the thickness ratio. The major effect pf interfacial diffusion is the overall reduction of the intensities of high-order Bragg peaks. However, the atomic concentration profile correlates with their relative intensities. The uncorrelated roughness is responsible for the increased linewidths of the Bragg peaks and the increase of the relative intensities of the subsidiary peaks to those of the Bragg peaks. Based on the above results, we present an analysis of the experimental XRD data in order to deduce the structural parameters of a molybdenum-silicon MLSM.