Collagen from bone was prepared by several methods. For modern and well-preserved bone the δ13C and δ15N of collagen replicas obtained after HCl or EDTA demineralization were similar to those obtained with a gelatinization procedure. However, in more poorly preserved fossil bone the δ13C and δ15N varied among the different protein extracts. The yield of collagen obtained with EDTA demineralization was consistently higher than extraction procedures that used HCl. The δ13C of individual amino acids separated from the collagen of modern and fossil whale bone varied up to 17%., and the δ15N from the same amino acids ranged over 47%. The δ13C and δ15N of most amino acids clustered closely to the average of the HCl insoluble collagen. The δ13C of the major amino acid in collagen, glycine, differed from the average HCl insoluble collagen by approximately 8%. in the fossil whale and 14%. in the modern whale. The δ15N of glycine differed from the average HCl insoluble values by approximately 4%. in the fossil whale and 7%. in the modern whale. Thus, diagenetic changes that alter the ratio of glycine to other amino acids in bone can be expected to perturb the values for carbon and nitrogen isotopes.