The binding behavior of substituted 1,4-bis(pyridinium)butane derivatives (X-Py(CH(2))(4)Py-X, X = H, 2-methyl, 3-methyl, 4-methyl, 2,6-dimethyl, 4-pyridyl, and 4-COOEthyl) 1(2+)-7(2+), with negatively charged carboxylatopillar[5]arene (CP5A) has been comprehensively investigated by (1)H NMR and 2D ROESY and UV absorption and fluorescence spectroscopy in aqueous phosphate buffer solution (pH 7.2). The results indicated that the position of the substituents attached on pyridinium ring dramatically affects the association constants and binding modes. 3- and 4-Substituted guests (1(2+), 3(2+), 4(2+), 6(2+), 7(2+)) form [2]pseudorotaxane geometries with CP5A host, giving very large association constants (>10(5) M(-1)), while 2,6-dimethyl-substituted 5(2+) forms external complex with relatively small K(a) values [(2.4 ± 0.3) × 10(3) M(-1)] because the 2,6-dimethylpyridinium unit is too bulky to thread the host cavity. Both of the binding geometries mentioned above are observed for 2(2+), having one methyl group in the 2-position of pyridinium. Typically, the association constant of [2]pseudorotaxane 1(2+)⊂CP5A exceeds 10(6) M(-1) in water, which is significantly higher than those of previously reported analogues in organic solvents. The remarkably improved complexation of bis(pyridinium) guests by the anionic host was due to electrostatic attraction forces and hydrophobic interactions.