Lymphoid organs are integral parts of all vertebrate adaptive immune systems. Primary lymphoid tissues exhibit a remarkable functional dichotomy: T cells develop in specialized thymopoietic tissues located in the pharynx, whereas B cells develop in distinct areas of general hematopoietic areas, such as the kidney or bone marrow. Among secondary lymphoid tissues, the spleen is present in all vertebrates, whereas lymph nodes represent an innovation particular to mammals and some birds. A comparative analysis of anatomical, functional and genomic features thus reveals the core components of adaptive immune systems. Such information has guided recent attempts at reconstructing lymphopoietic functions in vivo and in the future might inspire the development of new strategies for medical interventions restoring and modulating immune functions.