The spontaneous self-assembly of a novel comb-like amphiphilic copolyelectrolyte in water was studied by small angle neutron scattering and freeze fracture transmission electron microscopy. The copolymer was synthesized by randomly grafting pendant quaternized alkylamine moieties to a poly(styrene) chain. The effects of the grafting density and the length of the alkyls (C12–C18) on the structure were investigated systematically. The polymers were soluble over a broad range of grafting densities (35–80 mol%) where they assembled either into lamellae (35–55 mol%) consisting of a double layer of polymers or cylinders (65–80 mol%) formed by bundling of several chains. At higher concentrations, electrostatic repulsion drove smectic and hexagonal ordering of, respectively, the lamellae and the rods. TEM images showed micro-domains of stacked lamellae that were in some cases closed upon themselves to form onion-like particles. Exposure of hydrophobic patches at the surface due to defects of the self-assembly led to the formation of bonds between lamellae or cylinders. As a consequence visco-elastic solutions or hydrogels were formed at higher concentrations.