The biotransformation of rifamycin B to rifamycin S using immobilised whole cells of a Humicola sp. in a fluidised bed reactor exhibited a linear relationship between loading of the immobilised whole cells and conversion, in both batch and continuous operations; the conversion of rifamycin B was higher in batch than continuous operation for a given residence time. The immobilised whole cells were obtained by copolymerisation of the acetone-dried cells with acrylamide. They showed maximum activity of pH 7.8 and 50°C. It was found that aeration effects on the reaction in continuous operation were different from those in batch operation for the same residence time. In batch operation, the conversion of rifamycin B to rifamycin S increased with increased rate of aeration and reached a constant maximum value at aeration rates above 20.8 vvm. In continuous operation, the steady state conversion reached a maximum value in the range of aeration rate between 5.8 and 12.5 vvm; beyond this range the steady state conversion decreased steadily owing to cell leakage. The half life for the operational stability at 40°C was about 13 h.