For the last 25 years, haematopoietic cell transplantation (HCT) has been used as effective therapy for selected inborn errors of metabolism (IEMs), mainly lysosomal storage diseases and peroxisomal disorders. The main rational for HCT in IEMs is based on the provision of correcting enzymes by donor cells within and outside the blood compartment. The ultimate goal of HCT is to achieve a normal or near-normal life and normal neurodevelopment. HCT has been performed for more than 20 diseases. Only for Hurler syndrome, X-ALD and infantile Krabbe disease, are detailed studies available suggesting that HCT is indicated for carefully selected cases. Improvement of transplantation techniques and alternative therapies may change the recommended (contra-)indications for IEM. A recent example of emerging transplantation techniques is the fast availability of unrelated cord blood (UCB). UCB makes HCT feasible in patients with rapidly progressive neurological diseases. Because of the fast availability of UCB and therefore the ability to transplant shortly after diagnosis, there is no indication for patients in a moderate/good clinical condition to receive enzyme replacement therapy (ERT; in Hurler syndrome) prior to or during HCT and can ERT only be considered in patients with poor clinical condition. Mesenchymal stem cell infusions with HCT is an emerging technique, and might be interesting in halting the remaining defects after successful HCT. Improvement in HCT techniques and novel stem cell sources will significantly impact the safety and efficacy of this therapy as well as expand the list of candidate disorders. A good functioning worldwide registry would be necessary to measure the effects of the procedures performed in more detail.