In this study, the influence of different ionic environments on the dissociation of isolated αS- and β-CN fractions were evaluated and compared with the solubility of αS- and β-CN in solutions and CaCl2 precipitates of MCN, NaCN, and CaCN. The solubility and aggregation behavior was shown to be a balance of hydrophobic and electrostatic interactions that depend on the temperature, pH, and ionic strength. In prior studies, an approximately 4-fold yield in β-CN fractions derived from MCN was obtained by selective precipitation compared with that from commercial caseinate, indicating that the β-CN yield is dependent on the raw material. Evidence exists that the β-CN yield may be related to the solubility of β-CN in CaCl2 precipitate of MCN, NaCN, and CaCN at pH 4.5 and 2°C. Our results suggest that the yield of isolated β-CN fractions can be estimated by a simple solubility analysis before β-CN isolation to selectively choose future raw materials for β-CN isolation.