L-Cystine dimethyl ester dihydrochloride is primarily used in biochemical research and pharmaceutical development. It serves as a precursor or intermediate in the synthesis of peptides and proteins, aiding in the study of their structure and function. This compound is also utilized in the preparation of modified amino acids, which are essential for creating specialized peptides with enhanced stability or biological activity. Additionally, it finds application in the development of drug delivery systems, where it can be incorporated into carriers to improve the bioavailability and targeting of therapeutic agents. Its role in cross-linking and stabilizing peptide structures makes it valuable in the design of biomaterials and tissue engineering scaffolds.