The structure of amphiphilic hydrogels of copolymers of acrylic acid and n-alkylacrylate swollen by D2O was studied by small-angle neutron scattering (SANS). For most of the uncharged gels, a scattering peak is observed. It is attributed to the correlation between hydrophobic domains formed by self-assembled n-alkyl side chains. From the SANS data, the aggregation number of the hydrophobic domains was derived. It increases with increasing length of hydrophobic groups and also as a result of absorption of hydrophobic additives that are solubilized inside hydrophobic domains. The most important observation of this work consists of the fact that the introduction of charged groups into the gel leads to microphase separation with the formation of hydrophobic regions including several densely packed hydrophobic domains that alternate with hydrophilic regions swollen by water where most of the charged repeat units and counterions are located. The size of the hydrophobic regions decreases with increasing charge content. The microphase separation seems to be due to the effective interplay of two counteracting tendencies: hydrophobic association and electrostatic repulsion. When salt screening is added, the microphase separation disappears.