During the past decade, stem cell transplant has emerged as a novel therapeutic alternative for several diseases. If therapies are to be implemented in clinical settings, efficient scale-up of stem cells isolation methodologies would be crucial. A brief, process-oriented overview of the current most widely used technologies for stem cells separation is presented. This review classifies available methods into three broad categories: (1) isopycnic centrifugation, including density gradient and cell culture; (2) immunochemical, employing immune labeling; and (3) novel, tagless procedures. These groups are further subdivided into more specific techniques, highlighting their advantages and limitations. Particular cases in each category were selected to further compare the purification parameters of recovery, cell viability, purity, process time, and throughput. A particular focus on process scale-up feasibility and the challenges of this rapidly emerging field are stated. Lastly, likely directions are suggested for the development of new proposals which will make stem cells purification more advantageous and viable for clinical use. Copyright (c) 2011 Society of Chemical Industry