Our objective was to compare the Kjeldahl (i.e., reference method) and the SDS PAGE methods for determination of milk casein as percentage of true protein (CN%TP). The CN%TP is used as an index of casein degradation (i.e., lower CN%TP) and cheese yield capacity. Milks with lower CN%TP will have a higher frequency of off flavors. Milk samples from 16 Holstein cows were collected 4 times, once every 2 weeks for a total of 64 samples. Each milk sample was analyzed using the Kjeldahl method for total nitrogen (TN), non-protein nitrogen (NPN); and non-casein nitrogen (NCN), in duplicate. The TP (%), CN (%) and CN%TP were calculated. The SDS PAGE was used to determine the integration trace quantity (mm × OD) of the sum of all protein bands, the intact casein (CN) and casein proteolysis products (CNPP) bands of the gel for each sample. There are 2 ways to estimate CN%TP by SDS PAGE: 1) using only the intact CN bands divided by the total of all protein bands (i.e., CN%TP) and 2) using the sum of CN and CNPP divided by the total of all protein bands (i.e., CN+CNPP%TP). A t-test was performed to determine if there was difference between the mean CN%TP given by Kjeldahl versus the 2 estimates made using SDS-PAGE. The Kjeldahl CN%TP (mean = 81.05%, SD = 2.35) was higher (P < 0.05) than the SDS-PAGE CN%TP (mean = 75.80%, SD = 4.37). However, no difference (P > 0.05) was detected between Kjeldahl CN%TP (mean = 81.05%, SD = 2.35) and SDS-PAGE CN+CNPP%TP (mean = 80.42%, SD = 2.99). If the goal is to achieve agreement between results of Kjeldahl and SDS PAGE to estimate CN%TP for cheese yield, then the sum of the area of intact CN bands plus CNPP bands should be expressed as percentage of all protein bands. If the goal is to determine the extent of proteolytic damage that may relate to flavor defects and changes in functionality in dairy products, then the increase in SDS PAGE CNPP%TP is probably a more sensitive metric than Kjeldahl CN%TP.