Chymosin-induced coagulation of individual milk proteins during incubation at 30 °C was investigated using a proteomic approach. The addition of chymosin (0.006 units/mL) caused the milk proteins to coagulate after a 3 h incubation period. Approximately 88% of the milk proteins were coagulated into the milk pellet fraction, and the protein concentration of the milk supernatant fraction (MSF) decreased from 29.88 ± 0.12 to 3.74 ± 0.13 mg/mL. SDS-PAGE analysis showed that α(S)-, β- and κ-caseins in the MSF were almost depleted and that the total intensity of the protein bands corresponding to α(S)-caseins (α(S1) and α(S2)), β-casein, and κ-casein decreased from 1088.0, 901.5, and 617.0 area units to 6.9, 6.1, and 5.2 area units, respectively. Two-dimensional electrophoresis analysis indicated that α(S1)-, α(S2)-, β-, and κ-casein and a fraction of the β-lactoglobulin and serum albumin were found in the MSF following incubation with chymosin.