Sanfilippo syndrome type B, or mucopolysaccharidosis type IIIB, results from defects in the gene for α-N-acetylglucosaminidase (NAGLU); only a few mutations have been described. To rapidly identify most NAGLU mutations, an automated sequencing procedure was developed for analysis of the entire coding region, including exon-intron borders. By this method, eight affected families were studied, and the mutations in all 16 alleles were identified, more than doubling the number of published mutations for this gene. Eight mutations were described for the first time: five missense mutations (Y140C, Y455C, P521L, S612G, and R674C), two nonsense mutations (W675X and Q706X), and one 24-nucleotide insertion. Currently, 36% of all point mutations (8 of 22 alleles) involve R674, a codon having a CpG dinucleotide in the critical initial position. Other mutations were found in more than one family, raising the possibility that some may be relatively common and, possibly, ancient mutations. Six new nonpathological mutations were also identified and likely represent polymorphic variants of the NAGLU gene, two of which might alter enzyme level. Establishing genotype-phenotype relationships will be vital in the evaluation of experimental treatments such as gene therapy.