A subset of bone marrow cells that contains terminal deoxynucleotidyl transferase (DNA nucleotidylexotransferase; nucleosidetriphosphate:DNA deoxynucleotidylexotransferase, EC 2.7.7.31) can be identified in adult rats by immunofluorescence using affinity-column-purified antibody to homogeneous calf transferase. The transferase-positive cells comprise approximately 1.8% of bone marrow cells. Correcting the specific activity of terminal transferase in total bone marrow cells (0.21 units per 10(8) cells) for the percentage of transferase-positive bone marrow cells (1.8%) gives 11.7 units per 10(8) cells, a value approximately half that found for transferase-positive thymocytes. Fluorescence appears to be restricted to the nucleus of transferase-positive bone marrow cells, in contrast to the predominantly cytoplasmic fluorescence of small thymocytes from adult rats. Some large thymocytes contain intranuclear transferase fluorescence patterns similar to those seen in bone marrow. These thymocytes are especially numerous in neonatal rat thymus, where they are localized in the subcapsular region of the cortex. Thymocytes with combined patterns of nuclear and cytoplasmic transferase are also present. In addition, Thy-1.1 antigen, which is present on thymic and prethymic cells but not on the majority of post-thymic cells in the rat, is also present on transferase-positive bone marrow cells. The results suggest that the transferase-positive subset of bone marrow cells may contain the immediate progenitors of cortical thymocytes in the rat. The nuclear location of fluorescence may indicate the site of physiological activity of terminal transferase in thymocytes and their precursors.