ZnSe nanowires, 5–10 nm wide and several microns long, were fabricated by Au-catalyzed molecular beam epitaxy. Specially designed silicon–silicon dioxide substrates allowed an examination of individual nanowires with a combination of phase-contrast high-resolution transmission electron microscopy, Z-contrast scanning transmission electron microscopy imaging and energy-dispersive X-ray spectroscopy using a low-current electron probe with a diameter of 0.2 nm. Experimental results demonstrate direct evidence of Au incorporation within single-crystal sphalerite ZnSe nanowires.