The influence of Ca and Mg addition on the secondary structure of αS1-, αS2-, β- and κ-CN in solutions of individual and binary mixtures of caseins was investigated using FTIR spectroscopy. Both in individual and their binary mixtures, addition of Ca and Mg resulted in increase in β-sheet structures and decrease in triple helices and turns, implying binding of cations to similar sites. Binding of cations with phosphoseryl clusters with loop-helix-loop motifs explained the reduction in helical element. In addition, the binding of cations to electronegative regions reduced electrostatic repulsion, resulting in an increase in hydrophobic interactions accounting for increase in sheet structures. Compared with Mg, it seemed that Ca had more affinity for caseins, especially when they were in a binary mixture. The information presented here expands the present understanding of casein interactions.