Thymus is an important central lymphoid organ that plays a pivotal role in the generation of peripheral T-lymphocytes. Thymoma and thymus hyperplasia have been associated with various autoimmune disorders, mainly myasthenia gravis. There is no established relationship between thymus pathology and antiphospholipid syndrome; however, there are some reported cases of antiphospholipid syndrome associated with myasthenia gravis or following thymectomy. We present the case of a patient with antiphospholipid syndrome and thymic lymphoid follicular hyperplasia. We discuss the association between both entities and suggest a diagnostic approach of a patient with a radiological disorder of the thymus and antiphospholipid syndrome.