We herein report two cases of proteinase 3-anti-neutrophil cytoplasmic antibody (PR3-ANCA)-related nephritis in infectious endocarditis. In both cases, the patients were middle-aged men with proteinuria and hematuria, hypoalbuminemia, decreased kidney function, anemia, elevated C-reactive protein (CRP) levels, and PR3-ANCA positivity. Each had bacteremia, due to Enterococcus faecium in one and Streptococcus bovis in the other. One patient received aortic valve replacement therapy for aortic regurgitation with vegetation, and the other underwent tricuspid valve replacement therapy and closure of a ventricular septic defect to treat tricuspid regurgitation with vegetation. These patients' urinary abnormalities and PR3-ANCA titers improved at 6 months after surgery following antibiotic treatment without steroid therapy.