A 64-year-old woman complaining of severe lumbar pain was admitted to our hospital because of the finding of pre-existing mitral valve regurgitation on examination. Laboratory data revealed the proximal type of renal tubular acidosis, renal glucosuria, phosphaturia, generalized aminoaciduria and low-molecular-weight proteinuria. She did not have any cause of these tubular dysfunctions, and was diagnosed as adult idiopathic Fanconi syndrome. Dual energy X-ray absorptiometry (DEXA) revealed a reduction of bone mineral density in the lumbar spine to about 65% of the age-and gender-matched control value. Alkali agents (sodium citrate and potassium citrate), calcium lactate and 1 alpha-hydroxyvitamin D3 were administered. Bone mineral density estimated with DEXA improved with a reduction of serum alkali phosphate and disappearance of lumbar pain, and was restored to 82% of the age-and gender-matched control value after about 30 months of treatment. DEXA is useful for the long-term follow-up study of bone mineral density in a patient with Fanconi syndrome.