This chapter discusses the immunopathogenesis of autism. Two main immune dysfunctions in autism are immune regulation involving pro-inflammatory cytokines and autoimmunity. Mercury and an infectious agent like the measles virus are currently two main candidate environmental-triggers for immune dysfunction in autism. Genetically immune dysfunction in autism involves the major histocompatibility complex (MHC) region, as this is an immunologic gene cluster whose gene products are class I, II, and III molecules. Class I and II molecules are associated with antigen presentation. The antigen in virus infection initiated by the virus particle itself, while the cytokine production and inflammatory mediators are due to the response to the putative antigen in question. Environmental exposure to mercury is believed to harm human health, possibly through modulation of immune homeostasis. A mercury link with the immune system has been postulated due to the involvement of postnatal exposure to thimerosal, a preservative added in the measles, mumps and rubella (MMR) vaccines.