Flow cytometric techniques involving correlated dual parameter analysis of fluorescence and light scatter and transplantation bioassays were used to describe a series of cellular changes in thymus of young (1-4 mo old) AKR mice during development of mink cell focus-inducing (MCF) virus-accelerated leukemia. Three stages of leukemogenesis were defined before appearance of frankly leukemic mice. Stage 1, apparent 28-40 d after injection of MCF 69L1 virus, represented steady-state infection of thymocytes by MCF virus without apparent change in light scatter properties of the cells or in expression of alloantigens Thy-1, Lyt-1, Lyt-2, L3T4a, B2A2, or H-2K on the major thymocyte subpopulations. Expression of MCF virus was highest in the population of small cortical thymocytes. Stage II was observed at highest frequency 50-60 d postinjection and represented the emergence of a clonal population of cells with transformed properties which could be resolved from normal thymocytes by light scatter and expression of B2A2, H-2K, and gp70 antigens. Stage III was observed at highest frequency at 70 d postinjection, when considerable enlargement of thymus had occurred, and appeared to represent the outgrowth of fully transformed cells that replaced the normal thymocyte subpopulations. The alloantigen phenotype of blast cells from frankly leukemic mice did not differ qualitatively from that of stage II or stage III cells but displayed considerable heterogeneity with respect to quantitative expression of alloantigens and gp70. At least two populations of leukemic blasts could be resolved in the majority of primary thymomas analyzed. It is unclear whether these populations represent the outgrowth of independent clones of transformed cells or if they are related in some way. Our data are consistent with MCF virus-induced transformation of cells in the lineage to small peanut agglutinin-positive, cortisone-sensitive thymocytes, a subpopulation that predominates in the thymus and which is thought to be destined for cell death in situ.