Complexes of cationic amphiphilic cyclodextrins heptakis[2-(ω-amino-oligo(ethylene glycol))-6-deoxy-6-hexadecylthio]-β-cyclodextrin and heptakis[2-(ω-amino-oligo(ethylene glycol))-6-deoxy-6-dodecylthio]-β-cyclodextrin with DNA were examined by small-angle X-ray scattering and dynamic as well as electrophoretic light scattering. The first cyclodextrin forms bilayer vesicles in water, which, in the presence of calf thymus DNA, transform to a multilamellar complex. In this complex, the DNA lies between the two polar layers of the cyclodextrin’s protonated amino groups in alternation with the lipidic bilayers. The cyclodextrin with shorter lipid chains, in contrast, forms micelles in water, and electrostatic clustering of these about DNA does not affect their intrinsic structure. These results are relevant to the potential of such cyclodextrins in therapeutic gene delivery, showing that their self-assembly modes in isolation influence their complex formation with DNA and possibly their efficiency in promoting cell transfection.