Molecular analysis of the aspartylglucosaminidase (AGA) gene was performed on two Japanese siblings with aspartylglucosaminuria (AGU). They were the first Japanese patients diagnosed as AGU and up to now, no other patients with AGU have been discovered in Japan. AGA cDNA from one patient contained 7-nt (TCTCCAG) insertion between exons 3 and 4, which was identical with the 3'-terminal sequence of intron 3. Sequencing of amplified genomic DNA from both patients showed the same single base transition (A-->G) at the 5'-side adjacent to the insertion sequence. This mutation newly created a consensus AG dinucleotide at the 3'-splice site and caused alternative splicing of AGA pre-mRNA by leaving the 3'-terminal 7-nt of intron 3. BsmAI restriction site analysis of amplified genomic DNA indicated that they were homozygotes of this mutation. We conclude that splicing defect of intron 3 caused AGA deficiency in them.