Lysosomal storage diseases are disorders caused by deficiencies of enzymes responsible for the degradation of substances present in lysosomes. The loss of activity of a lysosomal enzyme leads to the accumulation of substrates within the lysosome, which is the initial step in the process leading to a lysosomal storage disease. Over fifty lysosomal storage diseases are known and have a collective incidence of approximately 1 in 7700 live births. One treatment for these diseases is enzyme replacement therapy, where the defective enzyme is replaced by a recombinant enzyme. Pharmacological chaperone therapy is an alternative treatment which uses small molecule inhibitors to stabilize the defective enzymes. The purpose of this project is to extend the study of lysosomal storage diseases into the field of molecular medicine by exploring the structure and function of human lysosomal enzymes, specifically those responsible for three variants of the mucopolysaccharidosis (MPS) family of diseases. These three enzymes fall into two categories: N-acetylgalactosamine-6-sulfatase (GALNS) and N-sulfoglucosamine sulfohydrolase (SGSH) are human lysosomal sulfatases while β-galactosidase (GLB1) is a glycosidase. In order to accomplish this goal we used a biochemical and structural biology approach. We solved the structures of SGSH and GALNS using X-ray crystallography and analyzed the mutations that lead to their respective diseases MPS III A and MPS IV A. This analysis revealed that these diseases could reflect protein misfolding since the majority of the mutations is located in the hydrophobic core of the proteins. The active site pockets of these enzymes have features such as charged amino acids and hydrophobic amino acids suitable for drug design. We determined that the small molecules galactose and 1-deoxygalactonojirimycin (DGJ) and 4-epi-isofagomine are competitive inhibitors of GLB1. Using the published crystal structure of GLB1, we present an explanation for the inhibitory effects of 4-epi-isofagomine.Through the structural analysis of the disease causing mutations and the identification of novel inhibitors; we hope to gain insight into the enzymatic mechanisms of these enzymes and the potential candidates for pharmacological chaperone therapy as treatments for the MPS family of diseases.