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Mastitis is generally recognized as an important factor that influences the quality of milk and dairy products. Milk from infected cows is characterized by increased Somatic Cell Counts (SCC) associated with changes in the components and properties of raw milk. The aim of this study was to evaluate the effects of SCC in raw milk on the casein fractions of semi-skimmed pasteurized milk during storage. Raw milk were categorized in SCC groups of low (<1×105 cells∙mL-1), intermediate (≈4×105 cells∙mL-1) and high cells (>75×104 cells∙mL-1). Four replicates of semiskimmed (1.3-1.4%) pasteurized milk within each SCC category were analyzed for composition, pH, titratable acidity and casein fractions by high performance liquid chromatography after 1, 7, 14, 21 and 28 days of storage. No effect of SCC was observed on the physical-chemical parameters and concentrations of αs-casein, β-casein and κ-casein in pasteurized milk during storage at 5ºC. However, chromatograms of milk samples containing high SCC (>75×104 cells∙mL-1) showed increased breakdown products of αs1-casein starting on the seventh day of storage. Results of this trial indicate that SCC in raw milk should not exceed 4x105 cells∙mL-1, to prevent the degradation of casein fractions in pasteurized semi-skimmed milk and the occurrence of quality defects during storage.