We have used atomistic molecular dynamics simulations to study the molecular-scale structure of poly(L-lysine) dendrimers homogeneously functionalized with naphthalene disulfonate caps from the first generation to the sixth generation. These dendrimers behave as typical dendrimers in poor solvent. As the generation number increases, there is a change from small molecule behavior to more polymer-like behavior. The first- and second-generation dendrimers, behaving as small molecules, are flexible, aspherical, and exposed to the environment, and their caps cluster together. Third- and fourth-generation dendrimers exhibit a transition toward polymeric behavior. The fifth-and sixth-generation dendrimers are large, essentially spherical globules, with a dense core, an irregular and highly grooved surface, and caps which are evenly distributed. Cap-cap interaction in all generations is favorable and is characterized by face-to-face naphthalene stacking.