To compare clinical and laboratory findings between patients with primary antiphospholipid syndrome (PAPS) versus secondary APS due to rheumatic fever (APS-RF) (according to Jones criteria). Seventy-three APS patients (Sapporo criteria) were enrolled, and demographic, clinical, and laboratory data were collected. Exclusion criteria were heart congenital abnormalities and previous infectious endocarditis. Patients were divided into two groups: PAPS (n = 68) and APS-RF (n = 5). The mean current age, disease duration, frequencies of female gender, and Caucasian race were similar in APS-RF and PAPS patients (P > 0.05). Remarkably, the frequency of stroke was significantly higher in APS-RF compared to PAPS patients (80% vs. 25%, P = 0.02). Of note, echocardiogram of these patients did not show intracardiac thrombus. No significant differences were found in peripheral thromboembolic events (P = 1.0), pulmonary thromboembolism (P = 1.0), miscarriage (P = 0.16), thrombocytopenia (P = 0.36), arterial events (P = 0.58), and thrombosis of small vessels (P = 1.0). There were no differences in the frequencies of comorbidities such as diabetes mellitus, hypertension, smoking, and hyperlipidemia in both groups (P > 0.05). The frequencies of lupus anticoagulant, IgG, and IgM anticardiolipin were similar in two groups. APS patients associated with rheumatic fever without infective endocarditis may imply a high stroke risk as compared with PAPS, and future studies are needed to confirm this finding.