Cationic, anionic, and nonionic cyclophane dimers, 1a, 1b, and 1c, covalently linked with fluorescent perylene diimide were synthesized, respectively, as a host for aggregation-induced multivalent effects on guest-binding. These PDI-linked cyclophane dimers 1a and 1b, especially 1c, formed self-aggregates in H 2 O-rich solvents through π-stacking interactions. Critical aggregation concentrations of 1a, 1b, and 1c in H 2 O were 4.0 × 10 −6 , 4.0 × 10 −6 , and less than 0.1 × 10 −6 M, respectively. The selfaggregates of the PDI-linked cyclophane dimers in H 2 O were several hundred nanometers in size by DLS and TEM measurements. In an aggregated state, 1a exhibited guest-binding abilities toward hydrophobic guests, such as 6-p-toluidinonaphthalene-2-sulfonate and 6-anilino-naphthalene-2-sulfonate. Moreover, anion-induced agglutination of 1a was observed upon the addition of phosphate ions, and its effectiveness was as follows: ATP > ADP > H 2 P 2 O 7 2− > AMP ≈ PO 4 3− > HPO 4 2− > H 2 PO 4 − . The contribution of the adenine base of the nucleotides as a guest moiety used for effective agglutination was confirmed by 1 H NMR spectroscopy.