Our aim is to elucidate the rare case of Wegener granulomatosis in childhood: its clinical symptoms, treatment, complications and outcome. We present clinical case of 12-year-old boy with affection of airways, kidneys, skin, joints and eyes. Diagnosis was confirmed on the basis of clinical picture, laboratory findings and ultrasound, x-ray, computed tomography, magnetic resonance imaging and biopsies of skin, nasal mucosa, renal tissues. We found four of five positive modified American College of Rheumatology diagnostic criteria. Conventional treatment with corticosteroids and cyclophosphamide eliminated renal symptoms, but the damage of the upper and central airways increased with development of subglottic stenosis. This complication was treated by urgent tracheostomy. Remission of disease was achieved with maximal doses of corticosteroids ant cyclophosphamide during 13 months from of symptoms onset. Peculiarities of our case were early onset, rapid development of life threatening symptoms, treatment with large doses of drugs and urgent surgery. Aforementioned active treatment did not prevent complications - steroid side effects, infections, bone fracture and subglottic stenosis.