Macroscopic models of bioprocesses are very useful to build engineering tools like simulators, software sensors or controllers. These models consist of a system of mass balances for macroscopic species involved in a reaction scheme, which can be determined analytically using a systematic procedure described in Hulhoven, Vande Wouwer, and Bogaerts (2005). Specifically, this procedure generates and compares all the C-identifiable schemes given a set of components for which concentration measurements are available. However, in such macroscopic models, component degradations (e.g. cell lysis) are often neglected, even though they can play a significant role. This paper proposes an extension of the above mentioned procedure which is aimed at the simultaneous estimation of a reaction scheme and component degradation rates. This extended procedure is applied to an industrial enzyme production within fed-batch bacterial cultures. (c) 2006 Elsevier Ltd. All rights reserved.