Aortic valve lesion is a common cardiopathy, which may have very diverse causes, from degenerative, congenital and infectious diseases to autoimmune conditions. We present a rare case of Takayasu arteritis and severe heart lesion due to the myxomatous degeneration of the aortic and mitral valve cusps associated with the development of infectious endocarditis (IE) complicated by abscess, fistula, valve perforation and recurrent acute decompensated heart failure in a young female patient. A combined use of histopathological and PCR analyses of valve tissues was critically important for differential diagnosis of the valve lesions, as it made it possible to identify the true cause of the structural cardiopathy associated with myxomatous degeneration and a prior IE. The presence of Takayasu arteritis has played an indirect though apparently decisive role by creating conditions for the development of immunosuppression and determining the disease severity and progression rate.