If the rich functionality of organic molecules is to be exploited in devices such as light-emitting diodes or field-effect transistors, interface properties of organic materials with various (metallic and insulating) substrates must be tailored carefully. In many cases, this calls for well-ordered interfaces. Organic epitaxy-that is, the growth of molecular films with a commensurate structural relationship to their crystalline substrates--relies on successful recognition of preferred epitaxial sites. For some large pi-conjugated molecules ('molecular platelets') this works surprisingly well, even if the substrate exhibits no template structure into which the molecules can lock. Here we present an explanation for site recognition in non-templated organic epitaxy, and thus resolve a long-standing puzzle. We propose that this form of site recognition relies on the existence of a local molecular reaction centre in the extended pi-electron system of the molecule. Its activity can be controlled by appropriate side groups and--in a certain regime--may also be probed by molecularly sensitized scanning tunnelling microscopy. Our results open the possibility of engineering epitaxial interfaces, as well as other interfacial nanostructures for which specific site recognition is essential.