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Renal manifestations associated with infective endocarditis (IE) may present with different clinical patterns, and the most common renal histopathological finding is diffuse proliferative and exudative type of glomerulonephritis, leading to hematuria and/or proteinuria. Renal failure due to crescentic glomerulonephritis (CGN) in children with IE is a very rare condition. We report here a 6-year-old boy, who had a history of cardiac surgery for pulmonary atresia and ventricular septal defect, presenting with the clinical findings of IE and hematuria associated with renal failure due to CGN. He was treated with a combination of intravenous (IV) methylprednisolone pulses and appropriate antibiotics, but also received one dose of IV cyclophosphamide. Complete serological, biochemical, and clinical improvement was achieved after 2 months of follow-up. Antibiotic therapy is the essential part of the treatment of IE-associated glomerulonephritis; however, this case also highlights the importance of aggressive immunosuppressive therapy to suppress the immunological process related with infection in this life-threatening condition leading to renal failure.