Studies of atomic arrangements in amorphous and crystalline, short period Mo-Ge multilayers using synchrotron radiation X-ray diffraction (transmission and reflection), supplemented by EXAFS, are described. Differential anomalous scattering and EXAFS were utilized to determine the environment of each species. Intermixing, as well as a BCC epitaxial Ge structure, are among the observed structural characteristics. A wide range of structural variations is present indicating that specification of the layer thicknesses or composition profile alone is insufficient for characterization of the multilayers.