Diagnosis of the combined course of diseases of the respiratory system and autoimmune diseases always presents certain difficulties in clinical practice. The article presents a clinical case that clearly characterizes the difficulties of diagnosing systemic lupus erythematosus (SLE) in atypical course and emphasizes the need for a broad multidisciplinary approach to patients with autoimmune pathology. In the case under discussion, the absence of skin manifestations typical for SLE led to the misdiagnosis of juvenile rheumatoid arthritis and incorrect therapy. Analysis of the disease’s course and clinical manifestations that occurred in the girl in adolescence, such as symmetrical arthritis, myalgia, general constitutional symptoms, fever, alopecia, anemia, in combination with positive antinuclear factor and presence of antibodies to denatured DNA, anti-phospholipid antibodies, reduction of the C3 component of complement, allowed to establish SLE diagnosis. The vigilance of any doctor regarding atypical onset of connective tissue disease will help to timely refer patient for consultation to rheumatologist and avoid possible errors in treatment. In this case, at the stage of complications development, the patient requires observation with multidisciplinary approach in treatment by a rheumatologist, pulmonologist, cardiologist, hemostasiologist, neurologist.