The molecular structure of novel ionic liquids based on cholinium amino acids (ChAA-ILs) has been analyzed. The polarization charge density for all ion pairs has been examined as a function of the hydrophobicity of the anion. The COnductor-like Screening MOdel σ-profiles and σ-potentials have been obtained and used to interpret the chemical behavior of ChAA-ILs. Some physicochemical properties such as density and viscosity have been estimated using the COnductor-like Screening MOdel for Realistic Solvation method. Furthermore, the effects of polarization on the molecular structure, physicochemical properties, and hydrophobicities have been evaluated. Finally, the results obtained have been compared with experimental data.