Understanding the relationship between genotype and clinical phenotype will clearly aid in the prognosis, treatment and counselling of patients with lysosomal storage diseases (LSDs). This, however, will require the establishment of widely accepted indices with which to score the severity of LSDs, as these diseases are characterized by their marked clinical heterogeneity. Even in the complete absence of a functional enzyme, presentation may be variable, depending on the patient's genetic background and on a range of epigenetic and environmental factors. Further difficulties in predicting disease severity and progression from the genotype arise from the rarity of these disorders, the low enzyme levels required for a normal phenotype and the relative lack of understanding of the pathophysiology of LSDs.