The CD45 phosphotyrosine phosphatase is expressed on T cells as multiple isoforms due to alternative splicing. The panoply of isoforms expressed is tightly regulated during T cell development and on mature peripheral T cell subsets following activation. We describe the analysis of comparative CD45 isoform expression levels on thymic and T cell subsets from the C57BL/6 mouse. Only four isoforms were expressed at significant protein levels: CD45R0, CD45RB, CD45RBC and CD45RABC, although trace amounts of others may be present. The expression of CD45RBC was about nine-fold higher on CD8(+) than on CD4(+) peripheral T cells, whereas CD45R0 expression was higher on CD4(+) T cells. We provide a general overview of the current models that have been proposed to explain the molecular actions of the different CD45 isoforms. Achieving a thorough understanding of the biological reasons for the existence and tight regulation of CD45 isoform expression in immune cells remains one of the outstanding challenges in the CD45 research field.