CD45 is a transmembrane protein tyrosine phosphatase found on nucleated hematopoietic cells. In humans, multiple protein isoforms of CD45 are produced by alternative mRNA splicing of exons 4, 5, and 6 coding for the extracellular portion. We measured all eight possible CD45 mRNA transcripts using RT-PCR in human thymocytes and T cell lines. We report that only six mRNA transcripts are present in T cells. The high mw CD45 mRNA transcripts containing exon 4 correlated with the stage of T cell maturation: abundant high mw transcripts (30.7% of all CD45 mRNA transcripts) were present in immature, CD3-4-8 triple-negative thymocytes which decreased (7.7%) in intermediate, CD4+8+ double-positive (DP) thymocytes and then increased (13.8% or 16.8%) in mature, CD4+8- or CD4-8+ single-positive thymocytes. In addition, there was a complex variation in the spliced mRNA transcripts coding for CD45R(O), CD45R(B), CD45R(BC), CD45R(AB), and CD45R(ABC) protein isoforms. High mw CD45 mRNA transcripts accumulated immediately prior to an important physiologic event such as thymocyte expansion. In addition, we identified linkage between RNA splicing of exons 5 and 6, and splicing of exon 5 only and exons 4, 5, and 6 in FACS-purified CD4+ and CD8+ thymocytes. These data support the developmental regulation of alternatively spliced CD45 mRNA transcripts and suggest that specific CD45 isoforms may play an important role at critical stages of T cell development.