An immobilised fungal bioreactor operated with pulsation of the gas-phase is proposed and operated at variable conditions for the continuous biological degradation of complex structures. In order to test the system, a hardly biodegradable dye (Poly R-478) was selected as a model compound and Phanerochaete chrysosporium as the ligninolytic fungus. High percentages of decolourisation--between 65% and 80%--under optimal conditions were achieved. Moreover, the system proved to have high stability with long operational periods (at least, 90 days). During the operation Manganese Peroxidase was the sole ligninolytic enzyme detected which points out this enzyme as the main substance responsible for decolourisation. The optimal conditions established were the following: temperature of 37 degrees C, use of oxygen, Mn2+ concentrations between 33 and 330 microM and exogenous H2O2 added in periodical pulses (as chemical reagent, 1 microM or as H2O2 enzymatically generated by 0.6 U L(-1) glucose oxidase and residual glucose).