Double-helical DNA was used as a template for the assembly of helical cyanine dye aggregates. The aggregates consist of cofacial dimers aligned end-to-end in the minor groove of the DNA. The effect of methoxy or fluoro substituents placed on the periphery of the cyanine dye heterocycles on aggregation both in water and on the DNA template was studied by UV-vis and circular dichroism spectroscopy. Methoxy groups were found to be stronger promoters of aggregation than fluoro, and a dimethoxy dye exhibited a higher propensity to aggregate compared with an unsymmetrical methoxy/fluoro dye. Semiempirical calculations supported the experimental observation of methoxy substitution favoring aggregation. These results indicate that dispersion and hydrophobic effects contribute more to dimerization/aggregation than do electron donor-acceptor effects.