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An autoimmune disease can affect virtually any part of the body, including the joints, muscles, kidneys, lungs, heart, and brain. An autoimmune disease can therefore manifest in countless ways. This can range from joint pain, muscle pain, and fatigue to fevers, rashes, and problems with organs such as kidneys and lungs.

If a patient has a particular symptom or problem that can not be explained by common conditions, a doctor might suspect an autoimmune disease as the cause, and refer the patient to a rheumatologist for further testing.