Isoflavones are plant-derived, biologically active compounds that are commonly used as natural drugs or diet supplements in the treatment of menopausal symptoms and as antioxidants. Recently, it was proposed that genistein (4′,5,7-trihydroxyisoflavone) may be used in the treatment of patients suffering from Sanfilippo disease (mucopolysaccharidosis type III), a severe genetic disorder for which no therapy is available. A pilot clinical study with this novel therapy, called ‘gene expression-targeted isoflavone therapy’ (GET IT), indicated that a standardized, genistin-rich soy isoflavone extract is effective in the treatment of such patients. Since various isoflavone-containing products are commercially available, the content of the main isoflavones were measured in such products. Extremely different amounts of isoflavones were determined in various products, from 0.13 to 39 mg per tablet. Only some of these products were found to be effective in inhibition of the synthesis of glycosaminoglycans (compounds whose degradation is severely impaired in mucopolysaccharidoses, including Sanfilippo disease) in cultured fibroblasts. Since in GET IT the dose of genistein is calculated per patient's body weight, the amount of this isoflavone in a tablet is crucial for this therapy. Therefore, the results presented in this report indicate that a careful choice of a proper isoflavone extract is necessary for GET IT. Copyright © 2009 John Wiley & Sons, Ltd.