The structure of hydrated Nafion membranes neutralized by N(CH3)(4)(+) ions has been investigated by the small angle neutron scattering technique. First, the spectra show that the counterions are condensed at the interface between hydrophilic and hydrophobic phases. More importantly, by applying a contrast variation method, the normalized scattered intensity of membranes swollen in several D2O/H2O mixtures was analyzed. The N(CH3)(4)(+) counterions were used as a probe to identify the nature of the scattering entity that is polymeric aggregates surrounded by ionic groups and water molecules, contrary to the generally accepted model. This new insight into the Nafion structure will allow one to reconsider the swelling process and the degree of mesoscopic orientation in such perfluorinated systems.