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Introduction Infective endocarditis (IE) has been reported to mimic granulomatosis with polyangiitis (GPA) and to test positive to antineutrophil cytoplasmic antibodies (ANCA), which may lead to a misdiagnosis and inappropriate treatment. Case presentation We report a case of a 59-year-old man admitted for purpura, gangrenous digital infarcts and glomerulonephritis. The diagnosis of IE was initially considered on the basis of heart murmur and two positive haemocultures to corynebacterium. Ineffectiveness of antimicrobial therapy and further neurological and nasal manifestations supported the diagnosis of GPA. Conclusions IE should be ruled out before initiation of immunosuppressive treatment. If the disease progresses despite antimicrobial treatment, vascular diseases should be rapidly taken into account in differential diagnosis and treated early to avoid fatal complications.