Germinal centres are receiving renewed attention following recent intravital multi-photon imaging studies. These data have shed new light on longstanding questions about the spatial organisation of germinal centres, B-cell migration, selection and differentiation. Mathematical models have proven invaluable in the analysis of intravital motility data, and have predicted novel B-cell selection mechanisms that are now supported by experimental findings. We argue that mathematical modelling adds a different vantage point to experimental data and provides a quantitative and systematic analysis of hypotheses and theories in immunology. Furthermore, the well-characterised nature of the germinal centre provides an excellent proving ground for mathematical modelling.