BACKGROUND: In this work, the scale-up of the biodesulfurization process at rest from shaken flask to stirred tank bioreactor cells has been studied taking into account the influence of the hydrodynamic conditions of the oxygen transfer rate. RESULTS: Different hydrodynamic conditions to carry out the biodesulfurization in a stirred tank bioreactor have been studied and compared with the results obtained in a shaken flask. The best results were obtained at a stirrer speed of 400 rpm and an air flow rate of 2 vvm. The oxygen transfer rate has been found to be the rate-limiting step, and there is a critical value, determined by a value for the volumetric mass transfer coefficient (k(L)a) of around 1.4x10(-2) s(-1), which cannot be exceeded without affecting the biodesulfurization process. CONCLUSION: The 4S biodesulfurization pathway is highly sensitive to oxygen availability, even under oxygen limiting conditions. Results obtained in a shaken flask have been reproduced satisfactorily in a stirred tank bioreactor by combining different hydrodynamic conditions and the constant-k(L)a scale-up criterion has been used to validate this approach. (C) 2014 Society of Chemical Industry