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Hypophosphatasia is a rare disease characterized by defective bone mineralization due to deficiency of tissue-nonspecific alkaline phosphatase. The patient was an 8-day-old male infant who presented with seizure since that day. Other symptoms included respiratory failure, requiring the use of a mechanical ventilator. Physical examination revealed a large bulging anterior fontanelle, soft skull bone, and radial deviation of both wrists. Laboratory examination showed normal serum calcium, low parathyroid hormone, normal 25-hydroxy vitamin D, and severely low alkaline phosphatase levels. Skeletal X-ray revealed dysplasia of the skull and cupping of the epiphysis of the limbs. Two heterozygous mutations (c.1052A>G, c.1559delT) of the ALPL gene were identified by Sanger sequencing. Thus, we report a case of confirmed lethal perinatal hypophosphatasia in Korea.