Formamidine disulfide dihydrochloride is primarily used in biochemical research as a reducing agent. It helps in breaking disulfide bonds in proteins, which is crucial for studying protein structure and function. This chemical is also employed in the preparation of samples for electrophoresis, ensuring proteins are in their reduced state for accurate analysis. Additionally, it finds application in the synthesis of certain pharmaceuticals, where it acts as a key intermediate in the production process. Its ability to stabilize reactive intermediates makes it valuable in organic synthesis, particularly in the development of complex molecules.