Long term effects of smallpox (besides death) were scarring of the skin, blindness, and deformity of the limbs due to arthritis. Smallpox is the only communicable disease that has been eradicated- it is gone. Long term effects of smallpox (besides death) were scarring of the skin, blindness, and deformity of the limbs due to arthritis. Smallpox is the only communicable disease that has been eradicated- it is gone.