Objective – To study the, clinical characteristics and diagnostic evaluation, in two patients suffering with Sanfilippo syndrome. Design– Descriptive study Materials and methods– Molecular analysis of the α–N–acetylglucosaminidase gene in two Indian patients with Sanfilippo disease was carried out. Disease–causing mutation was found in NAGLU gene in both patients, confirming the diagnosis of mucopolysaccharidosis type III. The parents of both patients had consanguineous marriage. The families were from Aurangabad district of Maharashtra state. First patient had c.1364A>C (p. Tyr455Ser) mutation and different mutation at same allele already reported in literature. Second patient had c.1915delinsTT (p. Glu639LeufsTer46) variant on DNA analysis. The particular variant was not detected before in literature. Hence, we report a novel variant in NAGLU gene causing MPS IIIB. Conclusion– Identifying disease causing variant in MPS III patients is important to confirm the diagnosis, provide recurrence risk in future pregnancies and offer prenatal testing for couples who are carrier for the variant.