Recent advances in the molecular study of beta-galactosidase deficiency (GM1-gangliosidosis and Morquio syndrome type B) are reviewed. Until now, 14 different mutations have been found in the beta-galactosidase gene in patients with this disorder. Gene mutations are heterogeneous, but common and specific mutations have been identified for three types of protracted clinical course; 51Ile-->Thr mutation for Japanese adult/chronic GM1-gangliosidosis, 201Arg-->Cys for Japanese late infantile/juvenile GM1-gangliosidosis and 273Trp-->Leu for Caucasian Morquio syndrome type B. These phenotype-specific mutant genes produce mutant proteins with significant residual enzyme activity, whereas mutant proteins associated with infantile GM1-gangliosidosis patients show complete loss of enzyme activity. The phenotypic variations of this disorder may be related to different mode of intracellular processing and turnover of mutant enzyme proteins.