Antiphospholipid antibodies (APA) are often associated with severe clinical manifestations, especially in the setting of systemic lupus erythematosus (SLE). Here we have investigated the prevalence of anticardiolipin antibodies (aCL) and lupus anticoagulant (LA) in paediatric patients affected with SLE, JCA and overlap syndromes (OS) and correlated the presence of aCL and LA with clinical features. aCL were assayed by enzyme-limited immunoassay; LA was determined by activated partial thromboplastin time and the kaolin clotting time test. aCL and LA assays were performed in parallel on at least two occasions over a 7-30-month follow-up. Fifteen out of nineteen (79%) SLE patients had aCL and 8/19 (42%) had LA. Six SLE patients displayed manifestations that were APA-related: deep venous thromboses, autoimmune haemolytic anaemia, pulmonary hypertension, neurological alterations. Five out of six symptomatic patients had both LA and high-titre aCL. In contrast, JCA and OS patients had usually low-titre aCL, no detectable LA and no APA-related manifestations. aCL persisted at high titre over time in SLE patients, but was only transiently detected in JCA and OS patients. This study shows that the simultaneous positivity for LA and high-titre aCL allows the identification of paediatric SLE patients who are at risk not only for thrombosis, but also for other APA-related clinical features.