This report deals with a 25-year-old female patient, who was admitted to a medical centre with complaints of fatigue and arthralgia. A non-homogeneous mass originating from the posterior papillary muscle and reaching the posterior and anterior cusps of the mitral valve was evident on the patient's echocardiogram. Her intractable fever, despite adequate antibiotic therapy, led us to consult with the cardiac surgeons. A mitral valve replacement was performed on the 8(th) day of admission. The pathological examination of the mitral valve and the vegetative lesion revealed the presence of organized thrombus and infective endocarditis. The patient had a history of oral contraceptive use for one year and at genetic examination we detected a heterozygous prothrombin mutation (G20210A). The association of infective endocarditis with native mitral valvular thrombosis in a case with prothrombin mutation and history of oral contraceptive use encouraged us to share our experience with our colleagues.