The ability to track antigen (Ag)-specific lymphocyte populations in vivo has greatly increased our understanding of the location and functional status of these cells throughout the course of an immune response. Recent technical advances have enhanced researchers' capability to follow migration, activation and cellular interactions of Ag-specific lymphocytes in situ. It is now possible to monitor changes in T cell subsets, co-stimulatory molecules, and chemokine expression within the physiological context of secondary lymphoid organs. Furthermore, the Ag-presenting cell-T cell interaction can be studied,thus dissecting the role and timing of Ag presentation of particular dendritic cell subsets in the initiation of the immune response. The capacity to adoptively transfer small populations of Ag-specific T lymphocytes has also increased our knowledge of the physiologically important role of regulatory T cells in autoimmunity and immunosuppression. New fluorescence imaging techniques such as multicolor video microscopy, laser scanning cytometry, and multiphoton tissue imaging have provided new ways in which researchers can track cellular changes within Ag-specific lymphocytes in vivo. This review summarizes some of the ways in which these techniques have led to discoveries in the role of signaling cascades, cell cycle progression, and apoptosis in maintaining an Ag-specific immune response.