We study the growth and internal structure of polyelectrolyte multilayers obtained by combining three polyanions with nine polycations of the ionene family, of systematically varied chemical architecture. We find that, contrary to a generally held belief, ordered organic multilayers are by no way exceptional, provided one of the polyelectrolytes bears groups which induce structure in water, such as long hydrophobic segments or mesogenic groups. However, this condition is not sufficient, as order will or will not emerge in the multilayer depending on the specific pairing of the polyelectrolytes. The results support the notion that layering in the multilayer results from some degree of prestructuring of a water-swollen layer adsorbed during each step of deposition. These findings pave the way to new possible uses of polyelectrolyte multilayers, for example, for applications requiring preferential alignment or strong confinement of specific functional groups.