In this paper we analyzed the clinical manifestation and course of the disease in 47 patients with systemic lupus erythematosus (SLE) and secondary antiphospholipid syndrome (APS) during prospective follow-up that lasted 2-5 years (mean 3.4). The most frequent features of APS were thrombosis (51%) thrombocytopenia (46.8%), and neuropsychiatric disorders (40.4%). These features were predominantly associated with elevated concentrations of IgG aCL isotype or with the presence of both IgG and IgM isotypes. Spectrum of neuropsychiatric disorders included mainly cerebrovascular ischemic disease (63%), but also some other, such as mental disorders and seizures, and, rarely, atypical migraine and transverse myelopathy. Thrombotic events in APS are the most significant for therapeutic and prognostic considerations. The treatment of basic disease (SLE) and conventional management of thromboembolic manifestation with heparin and/or dicoumarol (or warfarin) prevented neither the recurrent thrombosis in 9 patients (37.5%), nor the fatal outcome in 6 patients (12.8%). Further investigations and perhaps more aggressive approach to APS treatment are needed for better clinical care of these patients.