Auto-immune disorders that develop are not the only ones that can cause damage to the kidneys; contracted viruses, such as the human immunodeficiency virus (HIV) or hepatitis B and C, all can cause problems with the kidneys over time. About a third of all HIV patients will have abnormally high levels of protein in their urine. This is one indication that the kidneys could be taking damage. The blood may also show high levels of creatine, indicative of kidney troubles.