Besides pain and swelling, you may also feel tired, sick, or feverish. When you have an autoimmune disease, your immune system, which is meant to fight off germs, may attack your knees. For example, rheumatoid arthritis tends to affect hands and other joints in pairs on both sides of the body. Lupus goes after joints, muscles, and organs all over. Psoriatic arthritis often causes thick, discolored patches of skin, along with joint pain.