Childhood hypophosphatasia (HP) is an inborn error of bone metabolism, characterized by a reduced tissue-nonspecific isoenzyme of alkaline phosphatase (TNSALP). Bone mineral density (BMD) in childhood HP has not been reported so far. We measured BMD, in addition to markers of bone metabolism, in 6 boys with childhood HP (age 2-13 years) and in 10 parents and one sibling, each carrying the autosomal-recessive trait. BMD, measured by peripheral quantitative computed tomography (pQCT) and by dual-energy X-ray absorptiometry (DXA), was expressed as standard deviation from the normal mean (Z scores) and compared with bone mineralization by standard X-rays of the same locations. HP was confirmed by low TNSALP and its elevated substrates. In patients, BMD of the total body or spine, measured by DXA, was in the lower normal range. Total BMD of the distal metaphyses of the radius, measured by pQCT, was normal (Z score: mean +1.5). However, trabecular BMD of both radius (Z score: mean +4) and femur was grossly elevated. In parallel, X-rays showed reduced transradiancy of the radial and femoral metaphyses in all patients. In parents of patients with HP, BMD was in the lower normal range. Only one father had a decreased lumbar BMD. The discrepancy in BMD between cortical and trabecular bone of the metaphyses in patients was not present in their relatives. TNSALP levels in all first degree relatives were just below or in the lower normal range. The markers of bone turnover hydroxyproline and free deoxypyridinoline in urine were normal in patients and relatives. Hypermineralization/sclerosis of trabecular bone might serve as a compensation for a mechanically incompetent bony structure due to an impaired mineralization of cartilage caused by the genetic deficiency of alkaline phosphatase.