The electrostatic complexes of polyanionic DNA with dendrimers have been considered as a class of nonviral vector for gene therapy. The gene transfection efficiency has been believed to be influenced by the structure of the complex. In this study, we have systematically characterized the supramolecular structures of the complexes of DNA duplexes with poly(amido amine) (PAMAM) dendrimers with generation two (G2) and three (G3) in pure water using small-angle X-ray scattering. The structures were examined as a function of the charge density of the dendrimer expressed by its degree of protonation (dp) and the molar ratio of the amine groups of dendrimer to the phosphate groups of DNA (N/P). The DNA chains in all complexes under study were found to self-organize into two-dimensional hexagonal or square lattice. In general, hexagonal phase was the favorable structure for G2 complexes, while the DNA in G3 complexes tended to organize into a square lattice. Interesting transitions between the columnar mesophases with respect to the changes of N/P ratio and dp have been identified. The geometric features of the dendrimer molecules accommodated within the interstitial tunnels of the DNA lattices have also been revealed. The B conformation of DNA was effectively retained in the complexes in spite of the influence of the electrostatic interaction with the dendrimers.