This Chapter focuses on the use of isoflavones molecules to treat mucopolysaccharidoses (MPS) which are lysosomal storage diseases (LSDs). LSDs are inherited genetic disorders characterized by the deficiency of one enzyme involved in the catabolism of macromolecules, leading to the accumulation of its substrates in cell lysosomes. MPS are characterized by lysosomal accumulation of mucopolysaccharides (also called glycosaminoglycans or GAGs). They can be lethal disorders, some of them being characterized by severe neurological impairment. Recently, genistein, a molecule from the isoflavones family, has been identified as a promising drug medicine to reduce GAG accumulation in cells derived from MPS patients, as well as in several MPS mouse models. The first clinical results even indicated significant improvements in cognitive functions and behavioral symptoms of treated patients. Moreover, additional studies have highlighted the potential of different isoflavones and flavonoids as therapeutical molecules for MPS, either used alone or in combination. This overview suggests that isoflavones may be of potential benefit for the treatment of MPS diseases.