We report the case of a 37-year old man presenting with a left ventricular cardiac thrombus in the setting of subclinical paroxysmal nocturnal hemoglobinura (PNH) developing two years after immunosuppressive therapy for thymoma-associated aplastic anemia. The literature regarding the interplay between autoimmunity and immunosuppression, aplastic anemia, thymoma and the emergence of PNH is reviewed.