Nucleotide-induced permeability changes of oriented monolayers composed of the nucleotide receptors 4-amino-1-octadecyl-2-(1H)-pyrimidinone (1), 5-methyl-1-octadecyl-2,4(1H,3H)-pyrimidinedione (2), and 1-(2-heptylundecyl)-4-(8-(3-methylureido)-2-naphthyl)-amide-2-(1H)-pyrimidinone (3) were examined. These molecules are capable of binding guanosine, adenosine, and guanosine nucleotides, respectively, by multitopic hydrogen bonding. Monolayers were first formed at the air/water interface and then directly contacted with a highly oriented pyrolytic graphite (HOPG) electrode. The permeabilities of these membranes were evaluated with cyclic voltammetry, using [Fe(CN)6]4- as permeability marker. Selectively 5′-GMP-induced decreases in the permeability of the membranes based on receptor 1 or 3 were observed. On the other hand, decreases in the permeability of membranes based on receptor 2 were larger in the presence of 5′-AMP than of 5′-GMP. The permeability changes thus observed can be ascribed to repulsive electrostatic interaction between the marker anions and the negatively charged nucleotides that selectively bind to the electrically neutral membrane receptors. The ratios of the oxidation current decreases for solutions containing 3.0 mM 5′-GMP and for solutions containing 3.0 mM 5′-AMP were 1.30, 0.76, and 1.85 for monolayers based on receptors 1, 2, or 3, respectively. The monolayer based on receptor 3, which is capable of binding the guanine base by five hydrogen bonds, showed a higher 5′-GMP selectivity than the monolayer of receptor 1 with the cytosine residue. Similar nucleotide-induced permeability changes were observed for mixed multilayers of receptor 1 and octadecanol (4), as well as for mixed monolayers with receptor 2 and 4.