This paper presents the results of several experimental methods (FT-IR spectroscopy, UV–vis spectroscopy, fluorescence microscopy (FM), Atomic Force Microscopy (AFM)) evidencing structural changes induced in extremely diluted solutions (EDS), which are prepared by an iterated process of centesimal (1:100) dilution and succussion (shaking). The iteration is repeated until an extremely high dilution is reached, so that the composition of the solution becomes identical to that of the solvent—in this case water—used to prepare it.The experimental observations reveal the presence of supramolecular aggregates hundreds of nanometres in size in EDS at ambient pressure and temperature, and in the solid state. These findings confirm the hypothesis—developed thanks to previous physico-chemical investigations—that formation of water aggregates occurs in EDS. The experimental data can be analyzed and interpreted with reference to the thermodynamics of far-from-equilibrium systems and irreversible processes.