The agent-based approach to modelling bacterial population growth and development is a powerful tool for understanding the relationships between changes at the individual cellular level and overall population dynamics. Agent-based models are designed from the bottom-up, with rules and parameters created for the individual components of the simulation rather than for the population as a whole. The behaviour of the system is therefore an emergent property of the interactions between its constituent parts. In this chapter, an agent-based model called Micro-Gen is described, which can be used to investigate the effects of antibiotic resistance mechanisms on the response of bacteria to antibiotic treatment. The agent-based approach provides a rational framework for tracing back high-level pharmacodynamic parameters, such as the MIC (Minimum Inhibitory Concentration) of an antibiotic, to low-level biochemical information about the individual molecular components. The studies were carried out on a clinically significant species of bacteria called methicillin-resistant Staphylococcus aureus (MRSA), which are characterised by their increased resistance to many commonly prescribed β-lactam antibiotics. © 2011 Springer Science+Business Media, LLC.