Multiple sclerosis (MS) and anti-phospholipid syndrome (APS) are chronic, immune-mediated, relapsing-remitting disorders affecting young adults. APS is characterized by thrombosis and pregnancy mortality associated with anti-phospholipid antibodies. The diagnosis of APS may be difficult, and it is not uncommon for patients with APS to be misdiagnosed with multiple sclerosis. In this case report, we describe a patient who was diagnosed as having multiple sclerosis for eleven-year. Initially, the patient had neurological deficits with relapsing-remitting courses, like MS but he had not classic magnetic resonance imaging appearance of MS and absence of oligoclonal bands in the cerebrospinal fluid. He did not meet the 'dissemination criteria in time and place' specified in the MS diagnostic criteria. Also, he had an acute myocardial infarction and ischemic stroke at different times. The diagnosis of primary APS was made after the patient had thrombotic attacks, seizure and was positive for anti-phospholipid antibodies (aPLs) twice. Our observations raise awareness about the importance of the early and correct diagnosis of APS. When assessing MS patients, clinicians should consider APS, if the MS has atypical features.