The nanostructure of a series of 20 protic ionic liquids (PILs) has been investigated using small- and wide-angle X-ray scattering (SAXS and WAXS). The PILs contained alkylammonium, dialkylammonium, trialkylammonium, and cyclic ammonium cations combined with organic or inorganic anions. The presence of hydroxyl and methoxy substituents on the alkyl chains of the cations was also explored. Many of the PILs showed a nanostructure resulting from segregation of the polar and nonpolar components of the ionic liquid. It was found that this segregation was enhanced for longer alkyl chains, with a corresponding increase in the length scale, whereas the presence of hydroxyl groups on the alkyl chains led to much less ordered liquids. The broad range of protic ionic liquids studied allowed several structure-property relationships to be established. The solvophobic effect was shown to be dependent on the nanostructure of the PILs. These PILs support amphiphile self-assembly, and it was shown that the less structured PILs had more "water-like" behavior in the diversity of lyotropic liquid-crystal phases supported, and the thermal stability ranges for these phases.