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Aortic valve lesion is a common and may have 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 valves associated with development of infective 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 disease. The presence of Takayasu arteritis has played an indirect role by creating conditions for the development of immunosuppression and determining the disease severity and its progression.