Anatomical strategies that help cells to interact greatly increase the efficiency of the adaptive immune system. In vivo, antigens are presented in a complex environment, wherein their movements and those of antigen-presenting cells, T cells and B cells are subject to anatomical constraints. Specialized subcompartments appear to facilitate cell-to-cell contact and recognition and provide the most favorable milieu for signaling and induction mechanisms. How does the overall organization of a lymphoid organ facilitate the initiation and regulation of adaptive immune responses? This Review offers some answers to this basic question and focuses on the latest advances in our understanding of the functional anatomy of the lymph nodes, spleen and thymus.