Functional anatomy offers an attempt to exploit anatomical information as a platform from which to decipher mechanistic details of complex or multistep immunological processes. Immune function depends on structural organization, therefore this approach contributes to a comprehensive understanding of the immune system. Major advances in functional anatomy require progress in both experimental techniques and analytical equipment - largely synonymous to refinement of the anatomist's favorite tool, the microscope. Here, we describe how currently available techniques co-operate to gain new insights into the biology of secondary lymphoid organs.