Different aspects of the estimation and control of the respiratory quotient (RQ) have been investigated for the purpose of providing well characterized microaerobic, or oxygen limited, conditions in chemostat cultures. The RQ was controlled by changing the oxygen concentration in the inlet gas. The standard, steady-state equation for calculating the RQ in this case could not be used for dynamic RQ control. However, the dynamic characteristics of the equation could be considerably improved, by applying a first-order exponential filter to the inlet gas composition. Substituting the momentaneous inlet oxygen concentration for the filtered concentration in the standard gas balance equations resulted in favourable dynamic characteristics and high steady-state accuracy. Computer simulations showed that the sensitivity of the RQ to noise and bias in the oxygen analyses was acceptable for precision values typically achieved with mass spectrometry. A PID controller, and an adaptive pole placement controller, have been tried for the control of the RQ, calculated by the filtering procedure, during microaerobic ethanol production with Saccharomyces cerevisiae CBS 8066. The PID controller could not be used with constant control parameters, because the sensitivity of the RQ to the inlet oxygen concentration differed between different RQ setpoints. When the controller gain was adjusted for each RQ setpoint, the PID controller worked very well. The adaptive pole placement controller also worked well at all interesting operating conditions. In situ NAD(P)H fluorescence measurements indicated that the intracellular redox state is correlated to the RQ for RQ values in the range 10-30.