Structural modification of bovine mile beta-lactoglobulin (beta-LG) in aqueous 1-butyl-3-methylimidazolium nitrate ([bmim][NO3]) and ethylammonium nitrate ([EAN][NO3]) solutions has been investigated by Fourier transform infrared and circular dichroism spectroscopy. Remarkably, light ionic liquid (IL) concentrations (>15 mol %IL) caused formation of a non-native alpha-helical structure of beta-LG and disruption of its tertiary structure. Furthermore, while [bmim][NO3] promoted protein aggregation, [EAN][NO3] inhibited it probably owing to differences in the unique solution structure (nanoheterogeneity) of the ILs by the different cationic species. The IL-induced alpha-helical formation of beta-LG shows a behavior similar to the alcohol denaturation, but a disordered structure-rich state was observed in the beta-alpha transitions process by adding IL, in contrast to the case of an aqueous alcohol solution of protein. We propose that the molten salt-like property of aqueous IL solutions strongly support alpha-helical formation of proteins.