Argininosuccinate lyase (ASL) deficiency (McKusick 207900) is a rare autosomal recessive disorder affecting the urea cycle. The cardinal symptom in the neonatal form is progressive hyperammonemia, which is often life-threatening. However, clinical symptoms in the late onset form are quite heterogeneous. As well as measurement of ASL activity, analysis of the ASL gene is necessary to clarify the genetic basis of various phenotypes. We report a patient with late onset argininosuccinate lyase deficiency (ASLD) who had hepatomegaly and mildly increased level of ammonia. By mutation analysis of the mRNA and genomic DNA from the patient’s leukocytes, we identified a novel missense mutation 1395G>C in the homozygous state, which results in the exchange of a stop codon to tyrosine at amino acid position 465 (X465Y). This unique mutation causes an elongation of fifty amino acids in the C-terminal region of the ASL protein, and is likely related to a milder phenotype compared with previously reported mutations. In addition, this is the first report on mutation analysis in a Japanese ASLD patient.