Cystamine dihydrochloride is widely used in biochemical research, particularly in the study of protein structure and function. It serves as a cross-linking agent, helping to stabilize proteins and investigate their interactions. Additionally, it is employed in the preparation of disulfide bonds, which are crucial for maintaining the tertiary structure of proteins.

In the field of medicine, cystamine dihydrochloride has shown potential as a therapeutic agent for certain neurodegenerative disorders. It acts as a transglutaminase inhibitor, which may help in treating conditions like Huntington's disease by reducing the aggregation of misfolded proteins.

Moreover, this compound is utilized in the development of drug delivery systems. Its ability to form disulfide bonds makes it valuable in creating responsive drug carriers that release their payload in specific environments, such as those with high glutathione concentrations found in cancer cells.

Overall, cystamine dihydrochloride plays a significant role in advancing both basic scientific research and applied medical technologies.