The study was aimed at determining the effect of calcium chloride addition, temperature of milk pasteurization and a separation technique of milk components (centrifugation and ultrafiltration) on the content of nitrogen compounds and nutritive value of protein of whey and permeate obtained in the production process of cottage cheeses. Whey obtained after acid coagulation of milk supplemented with calcium chloride at a dose of 0.04% and pasteurised at a temperature of 90^oC/ 15 s, was characterised by statistically significantly lower (at α=0.05) contents of total nitrogen compounds, cysteine-cystine, leucine and lysine, compared to the whey obtained from milk pasteurized at 75^oC/ 15 s (with the addition of calcium chloride). Electrophoresis on polyacrylamide gel (Urea-PAGE) demonstrated reduced concentrations of β-lactoglobulin and α-lactalbumin in nitrogen compounds of whey as a result of their interaction with casein upon high pasteurisation of milk enriched with calcium ions. Due to the lower content of protein nitrogen compounds and essential amino acids compared to whey, including the limiting amino acid – leucine, the permeate was characterised by a lower nutritive value of protein expressed by values of chemical score (CS) and essential amino acid index (EAAI).