Micro-organisms play a central role in every ecosystem and in the global biomass cycle. They are strongly involved in many fields of human interest, from medicine to the food industry and waste control. Nevertheless, most micro-organisms remain almost unknown, and nearly 99% of them have not yet been successfully cultured in vitro. Therefore, new approaches and new tools must be eveloped in order to understand the collective behaviour of microbial communities in any natural or artificial setting. In particular, theoretical and practical methodologies to deal with such systems at a mesoscopic level of description (covering the range from 100 to 108 cells) are required. Individualbased modelling (IBM) has become a widely used tool for describing complex systems made up of autonomous entities, such as ecosystems and social networks. Individual-based models (IBMs) provide some advantages over the traditional whole-population models: (a) they are bottom-up approaches, so they describe the behaviour of a system as a whole by establishing procedural rules for the individuals and for their interactions, and thus allow more realistic assumptions for the model of the individuals than population models do; (b) they permit the introduction of randomness and individual variability, so they can reproduce the diversity found in real systems; and (c) they can account for individual adaptive behaviour to their environmental conditions, so the evolution of the whole system arises from the dynamics that govern individuals in their pursuit of optimal fitness. However, they also present some drawbacks: they lack the clarity of continuous models and may easily become rambling, which makes them difficult to analyse and communicate. All in all, IBMs supply a holistic description of microbial systems and their emerging properties. They are specifically appropriate to deal with microbial communities in non-steady states, and spatially explicit IBMs are particularly appropriate to study laboratory and natural microbiological systems with spatial heterogeneity. In this paper, we review IBM methodology applied to microbiology. We also present some results obtained from the application of Individual Discrete Simulations, an IBM of ours, to the study of bacterial communities, yeast cultures and Plasmodium falciparum-infected erythrocytes in vitro cultures of Plasmodium falciparum-infected erythrocytes