- A significantly high correlation between reduced activity of Annexin A5 by the flow cytometric assay (FCA) and the diagnosis of antiphospholipid syndrome (APS) has been reported. The aim of this study was to assess the clinical and laboratory significance of the Annexin A5 competition assay among patients with systemic lupus erythematosus (SLE). The FCA competition assay was performed on blood samples from 57 consecutive SLE patients. The FCA was performed according to a previously validated method. Forty-seven patients (82.5 %) had SLE without APS and ten (17.5 %) had SLE with APS. Twenty-four (42 %) of the patients had mean levels of AnxA5 fluorescence below the mean and standard deviation of the controls and were considered positive. SLE patients with a positive FCA were found to have an increased risk for a hypercoagulable or vascular state (86 % of the patients had cerebrovascular disease, 89 % had Raynaud’s phenomenon, and 80 % had deep vein thrombosis). The risk for any hypercoagulable or vascular state was significantly increased (P = 0.012, RR−2.3, 95 % CI 1.4–3.8). A positive FCA assay was found in 90 % of the patients with APS (P < 0.001), with a sensitivity of 90 % and a specificity of 68 % for this diagnosis. The positive and negative predictive values were 0.4 and 0.97, respectively. Correlations were found between positive FCA and positive Anti-Cardiolipin antibody (P < 0.001), and Anti-β2 glycoprotein I levels (P = 0.013). Our findings suggest that the FCA is a practical assay for the detection of clinically relevant APS among patients with SLE.