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Abstract Background Patients with persistent positive antiphospholipid antibodies (aPLs) and immune thrombocytopenia (ITP) hardly develop thrombosis but share many similar characteristics with antiphospholipid syndrome (APS). Methods This is a prospective cohort study consecutively enrolling thrombocytopenic patients with continuous positive aPLs. Patients developing thrombotic events are classified as the APS group. Then we compare the clinical characteristics and prognosis between aPLs carriers and patients with APS. Results This cohort included 47 thrombocytopenic patients with continuous positive aPLs and 55 with diagnosed primary APS. The proportion of smoking and hypertension are higher in the APS group (p = 0.03, 0.04, 0.03, respectively). The platelet count of aPLs carriers at admission was lower than APS patients [26 × 109/l (9 × 109/l, 46 × 109/l) vs. 64 × 109/l (24 × 109/l, 89 × 109/l), p = 0.0002]. Triple aPLs positivity is more common in primary APS patients with thrombocytopenia [24 (51.1%) vs. 40 (72.7%), p = 0.04]. Regarding the treatment response, the complete response (CR) rate is similar between aPLs carriers and primary APS patients with thrombocytopenia (p = 0.2). Nonetheless, the proportion of response, no response, and relapse differed significantly between the two groups [13 (27.7%) vs. 4 (7.3%), p < 0.0001; 5 (10.6%) vs. 8 (14.5%), p < 0.0001; 5 (10.6%) vs. 8 (14.5%), p < 0.0001, respectively]. In Kaplan–Meier analysis, primary APS patients had significantly more thrombotic events than aPLs carriers (p = 0.0006). Conclusions In the absence of other high-risk factors for thrombosis, thrombocytopenia could be an independent and long-lasting clinical phenotype of APS.