Probing the structure of material layers just a few nanometres thick requires analytical techniques with high depth sensitivity. X-ray photoelectron spectroscopy (XPS) provides one such method, but obtaining vertically resolved structural information from the raw data is not straightforward. There are several XPS depth-profiling methods, including ion etching, angle-resolved XPS (ref. 2) and Tougaard's approach, but all suffer various limitations. Here we report a simple, non-destructive XPS depth-profiling method that yields accurate depth information with nanometre resolution. We demonstrate the technique using self-assembled multilayers on gold surfaces; the former contain 'marker' monolayers that have been inserted at predetermined depths. A controllable potential gradient is established vertically through the sample by charging the surface of the dielectric overlayer with an electron flood gun. The local potential is probed by measuring XPS line shifts, which correlate directly with the vertical position of atoms. We term the method 'controlled surface charging' and expect it to be generally applicable to a large variety of mesoscopic heterostructures.