Some agro-industries generate wastewaters with very high COD concentrations and require two-stage biological treatment. Inert or residual organic constituents of these wastewaters, even at very low ratios, play a major role in the compliance of effluent standards. In this study, two strong wastes, citric acid plant effluent and cheese whey were tested for their inert COD content. The experiments showed that the first-phase anaerobic treatment provided a major decrease in the residual COD, but introduced significant amounts of particulate residual COD to the second phase. A newly developed procedure was used for the assessment of the soluble and particulate residual COD.