Biological nutrient removal systems (BNR) such as the Modified UCT (MUCT) process have an anaerobic, anoxic, and an aerobic zone for both biological phosphorus and nitrogen removal. In addition a prefermentation unit can be used to enhance these removals. In BNR systems the anaerobic zone is where volatile fatty acids (VFAs) are sequestered and transformed to polyhydroxyalkanoates (PHAs) and release of phosphorus occurs. In subsequent anoxic and aerobic zones PHA is degraded and phosphorus uptake occurs. The presence of high levels of VFAs in the anaerobic phase result in elevated amounts of PRA formation and phosphorus release. Prefermentation converts readily degradable influent COD to VFAs, and enhances PHA formation and anaerobic phosphorus release. In addition other fractions of the wastewater which also affect BNR performance are transformed. In this context, the changes in inert COD fractions of domestic wastewater treated with prefermentation were compared with those in the non-prefermented wastewater. Changes in the inert COD fractions of the raw domestic wastewater were subjected to fractionation. The prefermented and non-prefermented wastewaters fed two parallel and identical MUCT systems. The experiments discussed in this paper were done for a COD limited/septic wastewater. The fractionation procedure was done according to Germirli et al . The COD fractions in wastewaters are defined: initially inert particulate (XI), initially inert soluble (SI), particulate inert metabolic products (Xp), soluble residual metabolic products (Sp). The results show that the inert soluble fraction (sum of S, and Sp) was reduced from 11% of total influent COD (C-T0) to 7%. This has potential ramifications on process performance.