Autoimmune diseases represent a special group of the numerous and clinically different diseases. They appear as a result to the loss of immunological tolerance to the body's own antigens, from the synthesis of autoantibodies that attack its own cells. The causes of autoimmune diseases are still unclear, and many experts believe that most of them are largely caused by technological and cultural progress and removing human away from his natural environment (the so-called diseases of affluence). Also, there is no cure for the autoimmune disease that would permanently eliminate the cause, so the majority of patients remain on lifetime therapy, adjusted to their illness. Autoimmune diseases are classified into two main groups: organic specific and systemic diseases. While clinical picture of the organic specific autoimmune diseases depends on the organ affected, the clinical picture of systemic disease, especially in the early phase of the disease, is not so specific, so the diagnosis is often delayed. Diagnosis of autoimmune diseases is based on family and personal medical history, clinical picture and different diagnostic methods in vitro (radiogram, ultrasound) and in vivo (laboratory tests). Laboratory diagnosis involves determination of non-specific inflammatory indicators (SE, CRP, RF) and determining a large spectrum of autoantibodies. The general principles of the treatment are gradual application of four groups of medicines. Gradually treatment begins with anti-inflammatory medicines, than it continues with corticosteroids. If there is no improvement, treatment with the cytostatics should be adapted, and more recently biological medicines. During the treatment the side effects of drugs applied should be taken into account.