This study was conducted to evaluate changes in composition of whey proteins of Czech White Short-haired goat and East Friesian ewe milk and their comparison throughout lactation. Some differences in composition between ewe and goat milk were found. The results showed that the mean total protein (%), whey protein (g/100 g), and β-lactoglobulin (β-Lg, g/100 g) contents of goat milk were 2.75, 0.433, and 0.119 respectively and of ewe milk 6.36, 1.11, and 0.732 respectively. The contents of total protein as well as acid whey proteins in goat milk were nearly constant throughout the lactation period and fluctuated around the mean value while the contents of total protein as well as acid whey proteins in ovine milk were dependent on the period of lactation. The total protein content in ovine milk continuously increased during the lactation period. A higher content of ovine acid whey proteins was noticed at the beginning and in the final period of lactation. The average ratio of whey to total protein was 15.8  2.61% in goat milk and 17.4  2.68% in ewe milk and ranged from 13.0 to 20.4% in goat and from 14.0 to 20.8% in ewe milk. The total contents of two major whey proteins. α-lactalbumin and β-lactoglobulin (α-La + β-Lg = AG), averaged 87% of total whey protein, 92% in ovine milk. The main component of acid whey proteins in goat milk was α-La while in ovine milk the main component of acid whey proteins was β-Lg, however, at the end of the lactation period the content of β-Lg for both kinds of milk increased steeply, and the β-Lg/α-La ratio reached a maximum value of 1.94 in goat milk and of 9.74 in ewe milk. In addition, goat milk contains a similar amino acid profile to ewe milk but the amino acid pattern in whey proteins differs from that in milk. Total essential amino acids were approximately 40% of the total amino acids in goat and ewe milk as well as in goat and ewe whey.