In this study, we compared and reviewed the findings on lung perfusion scans performed in patients with systemic lupus erythematosus (SLE), systemic lupus erythematosus with associated antiphospholipid syndrome (SLE + APS), and primary antiphospholipid syndrome (PAPS), to evaluate the prevalence of pulmonary embolism in restricted samples of the patient groups. Lung perfusion scintigraphy with 99Tc(m)-macroaggregated albumin was performed in 31 patients (SLE = 7; SLE + APS = 14; PAPS = 10). The seven patients with SLE alone and the 10 patients with PAPS had normal perfusion lung scans. Six of the 14 SLE + APS patients showed a segmental uptake defect on multi-view perfusion scans. Thus, the SLE + APS patients were found to have a higher risk of pulmonary thromboembolism than the SLE alone and primary APS patients (P<0.05). The results of our study suggest that lung perfusion scintigraphy should be performed routinely in these patients, even in the absence of pulmonary clinical manifestations, to obtain baseline data for disease outcome and management.