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Osteoporosis in young men is extremely rare. In this report, we demonstrate a rare case of multiple vertebral fractures discovered in a young man with Budd-Chiari syndrome without prior history of trauma. A 29-year-old man was diagnosed as Budd-Chiari syndrome 12 years ago and underwent a mesocaval shunt to relieve the hepatic vein obstruction and was on warfarin therapy. He suffered from low back pain and it was not relieved by analgesics. A T-L spine X-ray revealed multiple compression fractures and the zscore at lumbar spine was -3.7 which is below the expected range for that age. The patient was treated with calcium, vitamin D and bisphosphonate, and showed clinical improvement. This case highlights the importance of the investigation for secondary osteoporosis in young adults with an underlying disease that alters bone metabolism.