We have developed hydrophobic-hydrophilic nanopatterns at electrified surfaces via the self-assembly of amphiphilic molecules. For this purpose, we selected 5-hexadecyloxy isophthalic acid: this neutral amphiphile forms hydrogen-bonded rows that are commensurate with the Au(111) surface. The alkyl chains are interdigitated. The molecular organization of these nanopatterns depends strongly on the substrate potential, which reveals the hierarchical nature of the assembly. The new hydrophobic-hydrophilic nanopatterns are of special interest as templates for the formation of nanostructures of higher complexity.