Goat cheeses were made from pasteurized (72 °C, 15 s) and high-pressure (HP)-treated milk (500 MPa, 15 min, 20 °C). At 45 days of ripening, cheeses made from both types of milk were similar in moisture, quality, electrophoretic profiles, water-soluble nitrogen, and total free fatty acid contents. Cheeses made from HP-treated milk had higher pH and salt, matured more quickly, as determined by formation of total free amino acids, and developed strong flavors. Reverse-phase high-performance liquid chromatography showed differences between the peptide profiles of the cheeses. Differences in small peptides and free amino acids indicated a higher extent of proteolysis in cheeses made from HP-treated milk.