The translation of experimental cell-based therapies to volume produced commercially successful clinical products requires the development of capable, economic, scaleable (and therefore frequently necessarily automated) manufacturing processes. Application of proven quality engineering techniques will be required to interrogate, optimise, and control in vitro cell culture processes to regulatory and clinically acceptable specifications. We have used a Six Sigma inspired quality engineering approach to design and conduct a factorial screening experiment to investigate the expansion process of a population of primary bone marrow-derived human mesenchymal stem cells on a scaleable automated cell culture platform. Key cell culture process inputs (seeding density, serum concentration, media quantity and incubation time) and important cell culture process responses (cell number and the expression of alkaline phosphatase, STRO-1, CD105 and CD71) were identified as experimental variables. The results rank the culture factors and significant culture factor interactions by the magnitude of their effect on each of the process responses. This level of information is not available from conventional single factor cell culture studies but is essential to efficiently identify sources of variation and foci for further process optimisation. Systematic quality engineering approaches such as those described here will be essential for the design of regulated cell therapy manufacturing processes because of their focus on identifying the sources of and the control of variation, an issue that is at the core of current Good Manufacturing Practice.