Self-association in water of biologically significant carbohydrate molecules is a controversial topic due to the strong solvation of these molecules in this solvent and the difficulty to experimentally detect these very weak intermolecular forces by biophysical techniques. Herein we report the tremendous ability of amphiphilic carbohydrate molecules to form complex three-dimensional architectures. We have experimentally observed the 3D self-assembly into multilayers of disaccharide neoglycolipid dimers on graphite by means of noncontact AFM and we have also theoretically modeled the interaction between two dimers in order to learn about the structure and composition of these layers. A simple bilayer structure as observed for many amphiphilic lipids was discarded by the experiments. Instead, based on the good agreement between experiments and calculations, we propose that multilayer formation takes place through the assembly of building blocks consisting of two dimers each. The fundamental key in the formation of this supramolecular structure is the complementarity between the van der Waals surfaces of the amphiphilic carbohydrate molecules, a result which differs from the most common idea that H-bonding interactions are prominent in carbohydrate-mediated interactions.