Brain in toxic encephalopathy. FLAIR magnetic resonance imaging (MRI) scan of an axial section through the brain of a 57-old patient with toxic encephalopathy caused by treatment with methotrexate for rheumatoid arthritis. Toxic encephalopathy is a degenerative neurologic disorder caused by exposure to toxic substances. Methotrexate is a common immunosuppressant used to treat autoimmune diseases such as crohn's disease and rheumatoid arthritis. Some adverse effects of methotrexate such as hepatic (liver) and renal (kidney) toxicity, are relatively common, however central nervous system toxicity caused is rare.