We present the formation, under ultrahigh vacuum conditions, of a three-dimensional organic architecture on a Au(111) surface based on the NH2?COOH interaction. The surface is first functionalized with a self-assembled monolayer (SAM) of an amine-terminated molecule (cysteamine, CA); then, a layer of benzoic acid (BA) is grown on top. We characterized this self-assembled structure by means of X-ray photoemission and absorption spectroscopy. The formation of a hydrogen bond between the two molecular species anchors the BA molecules to the CA. The structure is homogeneous in terms of its morphology and chemical properties. We also show that the structure (molecular orientation) of the BA SAM formed on the CA SAM is different from that of the BA SAM on the bare Au surface. The chemical recognition and molecular ordering nature of the BA?CA self-assembly makes it a promising candidate for the bottom-up parallel fabrication of hierarchically assembled nanodevices starting from functionalized building blocks.