Antibodies to prothrombin (aII) have been identified in patients with antiphospholipid antibodies, but their clinical significance is not well known. The aim of our study was to investigate their prevalence and association with clinical manifestations of the antiphospholipid syndrome (APS) in patients with primary APS or with systemic lupus erythematosus (SLE). A series of 177 patients with autoimmune diseases was studied: 70 with primary APS and 107 with systemic lupus erythematosus. A control group of 87 healthy volunteers were included in the study. aII were investigated in sera by an ELISA, using human prothrombin as antigen fixed in irradiated polystyrene plates. aII prevalence in patients with autoimmune disease was 47% (57% and 40% in patients with primary APS or with SLE, respectively) significantly higher than in controls (5%) (p<0.0001). In the whole series, thrombotic events were more prevalent in patients with aII (45% vs 28%; p=0.02). Moreover, aII was found to be an independent risk factor for arterial thrombosis (OR=2.4; p=0. 04). Similarly, in patients with SLE, aII were associated with both arterial and venous thrombosis (35% vs 14%; p=0.01), although only IgG-aII (OR=3.7; p=0.01) had an independent value as risk factor for thrombosis. However, a relationship between aII and thrombosis was not found in primary APS. aII were associated with thrombocytopenia only in patients with primary APS (OR=6.7; p=0.007). aII seem to be a serological marker of thrombosis in autoimmune diseases, mainly in SLE patients and/or in the arterial territory.