Room-temperature ionic liquids (ILs) are low-melting-point organic salts that, until recently, were thought to have homogeneous microstructure. In this work, we investigate nanoscale segregation of short (<C4) alkyl chain ILs using propylammonium nitrate (PAN) and ethylammonium nitrate (EAN). Structure peaks at q = 0.54 Å-1 for PAN and at q = 0.66 Å-1 for EAN, corresponding to Bragg spacings (D* = 2π/qmax) of 11.6 and 9,7 Å respectively, provide the first experimental evidence of nanoscale heterogeneity for ILs with alkyl chains less than C4. The observation that these ILs are not optically birefringent and the fits obtained suggest a disordered, locally smectic or sponge-like structure. Solvophobic interaction between alkyl groups is the most important factor for the production of nanoscale heterogeneities, but electrostatic and hydrogen bonding attractions between the amine nitrogen and the nitrate anion will also play a role.