The only known Japanese child with biotinidase deficiency was identified by newborn screening in Japan. He has 10.8% of mean normal serum biotinyl-hydrolase activity and trace biotinyl-transferase activity. The mutation results in 16% of normal cross-reacting material in serum with antibody to purified normal biotinidase. He is homozygous for a unique mutation, A1466 > C (Asn489Thr) in exon 4 of the biotinidase gene. The mutation appears to abolish a putative glycosylation site in a region in which other missense mutations have been identified, indicating that this region of the enzyme must be important for enzyme activity. This mutation may affect secretion or stability of the enzyme in serum. Interestingly, this child is now 8 years old, has not been on biotin supplementation for 3 years, and has remained asymptomatic.