Abstract: Functional low-and full-fat cheeses were fermented by Lactobacillus acidophilus and Streptococcus thermophilus. After ripening for 90d at 4 ℃ , the degrees of protein degradation had been analyzed in this experiment. Electrophoretic analysis showed that the two mentioned low-and full-fat cheeses, after ripened, were degraded more sufficiently than those sold in the market. What’s more, the degree of protein degradation of low-fat cheese was deeper than that of full-fat cheese, and the degradation content of the former also was more. Peptides RP-HPLC map of cheese indicated that, after ripened, there were still protein substances, as the same in milk, existed in low-and full-fat cheeses. However, degradation occurred in some of the protein and new peptides were produced. In addition, peptide components produced by low-and full-fat cheeses were different.