Cbz-D-allo-isoleucine is primarily used in peptide synthesis as a protecting group for amino acids. The carbobenzyloxy (Cbz) group shields the amino functionality during the synthesis process, preventing unwanted reactions. This compound is particularly valuable in the preparation of complex peptides and proteins, where selective protection and deprotection are crucial. Additionally, it finds application in the development of pharmaceutical intermediates, enabling the creation of biologically active molecules with high precision. Its role in organic synthesis also extends to the study of stereochemistry, aiding in the exploration of chiral molecules and their interactions.