Although the presentation of peptide-major histocompatibility complex class II (pMHC class II) complexes to CD4 T cells has been studied extensively in vitro, knowledge of this process in vivo is limited. Unlike the in vitro situation, antigen presentation in vivo takes place within a complex microenvironment in which the movements of antigens, antigen-presenting cells (APCs) and T cells are governed by anatomic constraints. Here we review developments in the areas of lymph node architecture, APC subsets and T cell activation that have shed light on how antigen presentation occurs in the lymph nodes.