Aspartylglucosaminuria (AGU) is an autosomal recessive lysosomal storage disease highly enriched in Finland where one mutation AGUFin major is responsible for 98% of the AGUFin alleles. Another mutation AGUFin minor has been identified in eight compound heterozygote patients who have AGUFin major mutation in their other allele. In addition four compound heterozygote patients have AGUFin major in one allele and unknown AGUFin mutation in the other allele. To study the origin of these mutations the haplotype analysis was performed on six patients with AGUFin minor mutation and four patients with unknown AGUFin mutation using nine microsatellite markers on the 7.6 cM chromosome region on 4q28-4qter. The haplotype data suggest that one founder mutation is responsible of all AGUFin minor alleles. Allelic association was also observed in AGUFin major chromosomes. Patients with unknown mutation did not share a common haplotype and therefore most likely have different origin.