This contribution reports the first X-ray standing wave structural characterization of self-assembled NLO-active chromophoric multilayers (SAMs). These siloxane-based self-assembled stilbazolium multilayers are intrinsically acentric and exhibit very large second-order nonlinear optical responses. The locations of bromide ions within the SAMs were precisely determined using X-ray standing waves generated by total external reflection from mirror surfaces as well as by Bragg diffraction from layered synthetic microstructures. The large coherent fraction (i.e., small Gaussian distribution width) of the Br- ions provides direct evidence for the high structural regularity of these self-assembled multilayers along the surface normal direction. These results are supported by atomic force microscopic (AFM) and X-ray photoelectron spectroscopic (XPS) studies which probe the structural regularity and chemical composition of SAMs, respectively. The anion surface coverage has also been measured in this study (2.5(5) x 10(14) Br-/cm(2)) and is in excellent agreement with the cation surface coverage measured by second harmonic generation (2(1) x 10(14) molecules/cm(2)). These results clearly demonstrate the utility of X-ray standing wave analyses as a quantitative microstructural probe for self-assembled mono- and multilayers, especially for SAMs with incommensurate structures.