Stem cell transplantation (SCT) is effective in the treatment of a wide range of malignant and nonmalignant conditions. Over the past decade there have been significant changes in: (i) the source of stem cells, (ii) the indications where transplantation has improved overall survival and (iii) regulation of all facets of transplant programmes. The stem cell processing laboratory plays an increasingly critical role in ensuring the best clinical outcome for any given transplant recipient. Consequences of a laboratory error may range from delayed haemopoietic engraftment to life‐threatening graft‐versus‐host disease to complete loss of product, with a serious adverse clinical consequence. To meet increasing demand and complexity the majority of stem cell laboratories are now regulated to ensure well‐developed validated SOPs, comprehensive staff training and education as well as utilization of proven accredited medical devices, commercial tests, environmental monitoring and analysis of product integrity at multiple intermediate stages.