Nanometer-scale structuring in room-temperature ionic liquids is observed using molecular simulation. The ionic liquids studied belong to the 1-alkyl-3-methylimidazolium family with hexafluorophosphate or with bis(trifluoromethanesulfonyl)amide as the anions, [C(n)mim][PF(6)] or [C(n)mim][(CF(3)SO(2))(2)N], respectively. They were represented, for the first time in a simulation study focusing on long-range structures, by an all-atom force field of the AMBER/OPLS_AA family containing parameters developed specifically for these compounds. For ionic liquids with alkyl side chains longer than or equal to C(4), aggregation of the alkyl chains in nonpolar domains is observed. These domains permeate a tridimensional network of ionic channels formed by anions and by the imidazolium rings of the cations. The nanostructures can be visualized in a conspicuous way simply by color coding the two types of domains (in this work, we chose red = polar and green = nonpolar). As the length of the alkyl chain increases, the nonpolar domains become larger and more connected and cause swelling of the ionic network, in a manner analogous to systems exhibiting microphase separation. The consequences of these nanostructural features on the properties of the ionic liquids are analyzed.