AbstractFunctional polyanions were prepared by copolymerization of sulfopropyl acrylate and sulfopropyl methacrylate with monomers bearing triaminopyrimidine or barbituric acid functionalities, respectively. Functionalized polyelectrolyte multilayers were assembled from these copolymers by stepwise alternating adsorption with poly(choline methacrylate). These multilayers are suited for molecular recognition of substrates that are complementary to the functional groups incorporated. Thus, multilayers containing triaminopyrimidine moieties selectively bind barbituric acid, and vice versa, when exposed to solutions of the 1:1 complex of barbituric acid and triaminopyrimidine. The molecular recognition process was monitored by UV/Vis spectroscopy, time‐of‐flight secondary ion mass spectroscopy (ToF‐SIMS), and photoelectron spectroscopy (XPS). Remarkably, after successful recognition and binding of the complementary substrates to the multilayers, the stepwise layering could be cont