Mucopolysaccharidosis (MPS) type VI, the lysosomal storage disorder caused by the deficiency of arylsulfatase B (ARSB) activity, occurs in humans, cats, and rats. To characterize the molecular lesion(s) causing MPS VI in rats, cDNAs encoding rat ARSB were isolated from a rat liver cDNA library. The nucleotide and deduced amino acid sequences of rat ARSB had approximately 80 and 85% identity with the human ARSB sequences, respectively. The chromosomal location of the rat ARSB gene was determined by PCR analysis of rat-mouse somatic cell hybrid panel. The ARSB gene was assigned to rat chromosome 2, where the locus for the MPS VI phenotype in rats has been localized by linkage analysis. To identify the mutation(s) within the ARSB gene causing MPS VI in rats, the ARSB sequence were amplified from affected animals and completely sequenced. Notably, a homoallelic one-base insertion at nucleotide 507 (507insC) was identified, resulting in a frame shift mutation and premature termination at codon 258. The presence of the insertion completely correlated with the occurrence of the MPS VI phenotype among 66 members of the MPR rat colony. Thus, we conclude that 507insC is the causative mutation in these animals and that the MPS VI rats are an authentic model of human MPS VI.