A case of a lesion of the central nervous system in Wegener's granulomatosis with neuritis of craniocerebral nerves, granulomas, vasculitis and foci of ishemic necrosis and hemorrhages in the brain tissue is reported. Diagnosis of Wegener's granulomatosis in a female aged 48 years was confirmed morphologically and by detection of specific antibodies. In spite of prednisolone (20 mg/day) and cyclophosphamide treatment (200 mg per week), hemiplegia, aphasia appeared which progressed and resulted in a death of the patient. Histologically lesions in many organs were found: middle ear, lungs, kidneys, brain, destructive vasculitis, necrotic foci and polymorphic lung granulomas, fibrosing alveolitis, polymorphocellular granulomas, multiple infarctions in the kidneys, endothrombovasculitis, necrotic foci and granulomas with glial reaction in the brain tissue.