We present a case of a 44-year-old female with systemic lupus erythematosus (SLE) with secondary antiphospholipid syndrome (APS). The patient died in the 15th year of the disease. The paraffin sections of the brain and spinal cord were examined using routine histological methods and immunohistochemistry with monoclonal antibodies against CD31, FVIIIAg and polyclonal antibodies IgG, fibrinogen and C3. Numerous thrombi-recent, organized and recanalized and focal vasculitis were seen. The immunopositive reaction in thickened vessel walls for CD31 and FVIIIAg indicated the process of the local incorporation of the thrombi. The immunoreactivity for fibrinogen, IgG and C3 suggests the immunological complexes formation in vessel walls, perivascular astrocytes and neurons.