Two-stage biological treatment schemes are often prescribed for pulp and paper mill effluents with high COD concentrations, in order to meet effluent standards. Recent conceptual developments in biological treatment of wastewaters indicate that the stoichiometry of the inert organic components is the key issue in performance predictions and the kinetics of degradable organic fraction play a relatively less important role in the compliance of effluent limitations. Besides, the differentiation between initially inert COD and inert metabolic products is very important in two-stage systems, as what is biodegradable for one phase may become non-biodegradable for the next phase in which a different microbial community is sustained. In this study a pulp and paper mill effluent is characterized in terms of its inert COD fractions and the changes induced by two-stage biological treatment to these fractions are observed.