Nephrotic patients are at risk of developing venous and arterial thrombotic complications. Pulmonary embolism due to affected deep leg veins is by far the most common event. Renal or cerebral vein thromboses have been described. Thrombosis of arterial vessels is less frequent. Mesenteric infarction is a rare but severe complication in patients with nephrotic syndrome (NS). We report a 7-year-old boy with a steroid-dependent (SD) NS and a homozygous mutation of methylenetetrahydrofolate reductase, increasing the risk of thromboembolic events. He developed a thrombosis of his superior mesenteric artery during his ninth relapse, which was responsible for a necrosis of 240 cm of his small bowel, necessitating resection of necrotic parts and double external ostomy diversion. Remission was achieved with pulse prednisolone therapy. Corticoids were reduced over 4 months progressively. Oral cyclosporin A (CyA) was initiated for long-term treatment. Due to a short bowel syndrome with severe malabsorption, even oral administration of 22.5 mg/kg per day CyA did not lead to sufficient plasma levels. Intravenous cyclophosphamide pulse therapy over 6 months led to a complete remission. No relapse occurred over a period of more than 5 months after the last cyclophosphamide pulse. Anticoagulation and screening for increased susceptibility for thrombotic events are necessary in every nephrotic patient. Intravenous cyclophosphamide pulse therapy is a useful alternative in SDNS with impaired intestinal absorption of applied immunosuppressive drugs.