Heterogeneity in the biomass distribution inside gel-immobilized cell systems was examined in detail by using modelling. The study was applied to Escherichia coli immobilized in thick agar membranes used in either discontinuous or continuous reactors. Two phenomena are mainly responsible for the heterogeneity : i) the substrate diffusion predominant during the earlier period at the edges of the biocatalytic structure and ii) the accumulation of the inhibiting product during the later period in the central area of the structure. The examination of the influence of the physiochemical parameters shows that, although the reaction flux is very weakly influenced by these parameters, heterogeneity is greatly enhanced when wither the initial cell concentration is increased, the substrate concentration is decreased, or the membrane thickness is increased. Continuous stirring tank reactor (CSTR)-type reactors also show a greater heterogeneity in the immobilized biomass distribution than discontinuous closed reactors in which the cell leakage in the external medium controls the system more. This may have great interest in many gel-immobilized cell systems and biofilm treatment in which the biomass distribution inside the biocatalytic structure is a very critical phenomenon.