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Although glomerular injury has been recognized as a prominent complication of cyanotic congenital heart disease (CCHD), the nephrotic syndrome is rarely observed. A 23- year-old male with CCHD presented with edema in the eyelids and ankles since three months. He was cyanotic at birth and was diagnosed as having persistent truncus arteriosus and atrial septal defect. On admission, blood pressure was 130/90 mmHg and heart rate 76/minute. Laboratory findings revealed 5 g/day proteinuria, hemoglobin 17.1 g/dL, hematocrit 55.5%, serum creatinine 1.8 mg/dL, total protein 4.1 g/dL, serum albumin 2.2 g/dL and hypoxemia. Renal biopsy was performed and showed global sclerosis and focal segmental glomerulosclerosis (FSGS). Phlebotomy was performed and prednisolone 1 mg/kg/day and losartan 100 mg/day were started. After three months, cyclosporine A (CsA) (5 mg/kg/ day) was added to the treatment with a proteinuria level of 5.9 g/day. On the eight month of treatment proteinuria was reduced to 1.9 g/day with a serum creatinine level of 1.5 mg/dL, and albumin 3 g/dL. In this rare case, partial remission which was achieved by CsA and angiotensin receptor antagonist showed the important role of glomerular hyperfiltration in the development of CCHD-associated FSGS. When the secondary FSGS causes were ruled out, CCHD should be kept in mind and echocardiographic assessment should be performed.