Enzyme replacement therapy (ERT) has been approved for 6 lysosomal storage diseases (LSDs) worldwide including Japan. These diseases include Gaucher disease (GD), Fabry disease, mucopolysaccharidosis (MPS) types I, II, and VI, and Pompe disease (PD). The efficacy and safety of ERT for LSDs has been confirmed by extensive clinical trials. However, there are still obstacles to successful ERT, such as immune reactions against the infused enzyme, mistargeting of enzymes rather than lysosomes, and intractable tissues. Regarding immune reactions, a negative impact of antibody formation on therapeutic effect has been reported for GD, Fabry disease, MPS type I, and PD. In PD, mistargeting of the enzyme was reported in a mouse model due to autophagic build up. Another challenge is intractable tissues, such as the brain and bone, which are key tissues in LSDs. Thus, control of immune reactions against therapeutic enzymes and control of autophagic build up are key issues to maximize the efficacy of ERT. Finally, the development of a new enzyme that effectively targets the brain and bone is very important to improve the quality of life of patients with LSDs.