Syphilis Complications. Complications Due to Syphilis. At its beginning stage, syphilis will cause sores called chancre in the body. Chancres are seen mostly in genital areas of the body. Syphilis can also cause rash, mild fever, fatigue, headache, sore throat, patchy hair loss, and swollen glands through the body. If left untreated syphilis can spread to all areas of the body. Syphilis most likely will affect the heart, eyes, brain, nervous system, bones, and joints.