Multilayer thin film structures for reflecting soft x-rays are now being fabricated in a number of laboratories. However, understanding of. the optical properties of these structures is presently limited by lack of knowledge of the microstructure of the layers, as well as of the details of the interfaces. In this paper we present results from our studies of multilayers grown by molecular beam epitaxy (MBE), characterized in situ by reflection high energy electron diffraction (RHEED), low energy electron diffraction (LEED), Auger, and x-ray photoelectron spectroscopy (XPS), and characterized ex situ by scanning tunneling microscopy (STM), transmission electron microscopy (TEM), x-ray diffraction, and Rutherford back scattering (RBS). In the case of Mo/Si multilayers, we observe the formation of an amorphous interfacial silicide, which can have a positive effect on the performance of these evaporated multilayer mirrors. We observe a contraction in the period of these multilayers as the deposition temperature is raised from 50 °C to 250 °C, corresponding to an increase in the thickness of the interfacial silicide. This contraction indicates that the silicide is more dense than the average atomic density of its components. We also discuss Ag/B and Pd/B multilayers, which have very similar theoretical performance. However, due to differences in the multilayer structures formed, the actual performance of multilayers made from these materials is radically different. The structural differences originate from different growth modes for Ag and Pd on B.