In this contribution we report on a structural investigation of the two-dimensional (2D) supramolecular organization of three bis-urea substituted thiophene derivatives, containing one, two, or three thiophene units, at the solution/graphite interface with scanning tunneling microscopy (STM); The compounds under investigation form highly ordered physisorbed monolayers. It is found that hydrogen bonding between the urea groups of adjacent molecules controls the spatial arrangement on the graphite surface. Molecular modeling and theoretical calculations demonstrate that the thiophene rings are tilted with respect to the surface and have partially overlapping pi -systems. This control of the 2D self-assembly is promising for future studies on the electronic properties of these molecules.