Molecular recognition of an anionic meta-cyclophane towards bioactive amines and related compounds has been studied by 1H NMR titration: the meta-cyclophane, which is functionalised by pendant arms, is 2,9,18,25-tetraoxo-4,7,20,23-tetrakis(carboxymethyl)-1,4,7,10,17,20,23,26-octaaza[10.10]metacyclophane; the bioactive guests studied are histamine, tryptamine, tyramine, phenethylamine, imidazole, histidine, phenylalanine and 4-aminobenzoic acid. Complex formation of a para-cyclophane isomer has also been studied for comparison. The meta-cyclophane forms a complex with histamine with a formation constant of 63 M− 1, while the complexes with the other amines have a smaller constant in the range of 1–24 M− 1; the compounds other than the amines have no interaction with the host. The major binding force for the complex formation is electrostatic interaction between the arm of the hosts and the arm of the guests. The aromatic group of a guest amine molecule is encapsulated into the cavity of a host molecule, and the deepness of the encapsulation is increased with the hydrophobicity in the order histamine < tyramine∼phenethylamine < tryptamine. In addition to hydrophobic interaction, the meta-cyclophane is supposed to have a dipolar interaction with a guest molecule. The combined effect of the three types of interactions stabilises the histamine complex of the meta-cyclophane. Complex formation of an anionic meta-cyclophane with bioactive amines including histamine, tryptamine, tyramine and phenethylamine was studied by NMR. Histamine forms the most stable complexes, as a result of a combined effect of electrostatic interaction, hydrophobic interaction and dipolar interaction, while tryptamine is most deeply included in the host cavity.