Mepacrine dihydrochloride dihydrate is primarily used in the medical field as an antimalarial agent. It effectively treats and prevents malaria by interfering with the growth of parasites in the red blood cells. Additionally, it has been employed in the treatment of giardiasis, a parasitic infection of the small intestine. Beyond its antiparasitic applications, it is also used in research settings as a fluorescent stain to highlight cellular components, particularly in studies involving DNA and RNA visualization. Its ability to bind to nucleic acids makes it a valuable tool in molecular biology and histology. In some cases, it has been explored for its potential anti-inflammatory properties in autoimmune diseases.