The article presents a clinical case of a 27-year-old woman with infectious endocarditis in vasculitis associated with antineutrophil cytoplasmic antibodies. Difficulties in the management of the patient are described, consisting in verifying the nature of changes in the heart (vegetation), as well as in determining the treatment tactics. Changes in the heart were regarded as infectious endocarditis. Adequate antibacterial therapy was carried out with a positive clinical and laboratory effect, with a significant decrease in vegetations on the valves, a decrease in the size of the formation in the aorta sinus, and a decrease in aortic regurgitation. The therapy of infectious endocarditis in granulomatosis with polyangiitis is difficult due to the need for a correct combination of adequate antibacterial therapy of infectious endocarditis and high doses of glucocorticosteroids and immunosuppressive drugs for autoimmune disease.