Water-soluble supramolecular inclusion complexes of alpha-, beta-, and gamma-cyclodextrin-bicapped C60 (CD/C60) have been investigated for their photoinduced DNA cleavage activities, with the aim to assess the potential health risks of this class of compounds and to understand the effect of host cyclodextrins having different cavity dimensions. Factors such as incubation temperature, irradiation time, and concentration of NADH or CDs/ C60 supramolecular inclusion complexes have been examined. The results show that alpha-, beta-, and gamma-CDs/C60 are all able to cleave double-stranded DNA under visible light irradiation in the presence of NADH. However, a difference in the photoinduced DNA cleavage efficiency is observed, where the cleavage efficiency increases in the order of alpha-, beta-, and gamma-CD/C60. The difference is attributed to the different aggregation behavior of the inclusion complexes in aqueous solution, which is correlated to the cavity dimension of the host cyclodextrin molecules.