Milk from two different breeds (Gokceada and Turkish Saanen) and three different starter culture systems (starter-free, mesophilic and thermophilic cultures) were used in the manufacture of Gokceada goat cheeses. Milk from the two breeds differed in dry matter, protein, fat and ash contents. These differences were reflected on the yield and chemical composition of the cheese. The pH values and soluble nitrogen fractions (in water, 12% trichloroacetic acid, and 5% phosphotungstic acid) were significantly influenced by the starter culture systems, but not the types of milk. The degradation of alpha(s)-caseins and its degradation products sharply increased after 60 days of ripening, especially in the cheese made using mesophilic starters. Greater changes were observed in RP-HPLC peptide profiles of the cheeses made using mesophilic starter cultures during ripening; however, the breed has minor effect on peptide profile. In conclusions, cheeses made using mesophilic starter culture exhibited different proteolysis patterns during ripening and the milk from Gokceada breed increased the gross composition parameters and cheese yield. (C) 2013 Elsevier B.V. All rights reserved.