In January 2009, a 70-year-old Japanese woman on long-term dialysis was admitted to our hospital for evaluation of a painful left leg. Maintenance dialysis was started in 1982, and parathyroidectomy was performed for secondary hyperparathyroidism in 2004. Most of her small intestine was resected because of superior mesenteric artery thrombosis in 2006, and the remaining small bowel only extended 50 cm distal to the ligament of Treitz. Parenteral nutrition was started after bowel resection. Fracture of her left leg occurred suddenly without any precipitating factors in January 2009, and iliac bone biopsy revealed severe osteomalacia with an increase of total osteoid volume (57.6%) (>15%) and no fibrous tissue (0%) (<0.5%). Although phosphorus and active vitamin D were administered intravenously to correct her hypophosphatemia and vitamin D deficiency, significant improvement was not achieved. This case indicates that when a patient on long-term dialysis with parathyroidectomy also suffers from short bowel syndrome, osteomalacia may become very severe. Lack of healing of the fracture, persistence of pain, and subsequent fracture even after vigorous treatment for low serum phosphate and calcitriol levels implied that these medications were not necessarily sufficient for this patient.