Benzamidine hydrochloride is widely used as a serine protease inhibitor in biochemical and biomedical research. It effectively inhibits enzymes such as trypsin, thrombin, and plasmin, making it valuable in preventing protein degradation during cell lysis and protein purification processes. Due to its specificity, it is often included in protease inhibitor cocktails to preserve sample integrity. It is also employed in studies involving blood coagulation and fibrinolysis pathways. Additionally, benzamidine hydrochloride serves as an intermediate in the synthesis of pharmaceuticals and other biologically active compounds. Its ability to cross cell membranes is limited, so it is primarily used in extracellular or cell-free systems.