The capillary electrophoresis separation of four inorganic anions (NO3-, I-, Br- and SCN-) was investigated over the whole range of methanol-water mixture composition. As the separation selectivity was strongly dependent on the solvent composition, the influence of ion-pairing and solvation phenomena was examined in depth in an attempt to explain this modification. First, a series of experiments was performed in methanolic background electrolytes, with counter-ions of different size. Ion-pair formation involving electrolyte ions was assessed to allow for a correction for free electrolyte ion concentration. Ion-pair formation constants between each inorganic anion and electrolyte counter-ion were next determined from the variations of the anion mobility as a function of the free counter-ion concentration. In view of the low values obtained, ion-pair formation alone failed to explain the selectivity variations. Solvation phenomena were then investigated with the help of a theoretical quantum model, the density functional theory (DFT), coupled with a polarizable continuum model to mime non-specific solvent effects. Whereas this model proved successful at predicting the mobility order at infinite dilution in water, it failed to predict the correct order in methanol.