Among 312 primary-APS patients, 143 (46%) had new thrombotic event classified to three patterns: (1) Arterial—associated with heart valve disease (OR 7.24, 95% C.I. 2.26–24.6), hypertension (OR 3, 95% C.I. 1.44–6.25), elevated anti-B2-GPI IgM (OR 1.04, 95% C.I. 0.996–1.08), arterial thrombosis at presentation (OR 1.74 95% C.I. 0.992–3.26), and older age (41 vs. 34 years, p < 0.001). This evidence concerns the gene CD40LG and autoimmune polyendocrinopathy.