The most recent mathematical models of microbial activity in heterogeneous biofilms are based on cellular automata. The main weakness of these models is that to obtain numerical solutions the operator must specify the rules governing microbial cell behaviour in the biofilm, and these rules are difficult to establish experimentally. To avoid this difficulty, we have used an alternative approach, discretizing biofilms into layers, to include the effects of biofilm heterogeneity on biofilm activity. This procedure conceptually converts heterogeneous biofilms into a stack of stratified layers of various densities, activities, and diffusivities, and can include some effects of biofilm heterogeneity, e.g vertical distribution of biofilm density, activity, and effective diffusivity. We present this model and selected examples of computational procedures illustrating it. We found that the activity of homogeneous biofilms can be lower, higher, or equal to the activity of stratified biofilms; since homogeneous biofilms do not exist, their properties have to be assumed. As expected, the model predicts that the growth-limiting nutrient penetrates deeper into stratified biofilms than it does into homogeneous biofilms. (c) 2005 Elsevier Ltd. All rights reserved.