We have identified a CD40-regulated gene, Clast6/E3/LAPTM5, by subtraction of cDNAs derived from resting and CD40 ligand-treated B cells. Clast6/E3/LAPTM5 is abundantly expressed in resting mature B cells but is rapidly and transiently repressed by treatment with CD40 ligand, a T helper signal that induces B cell activation. Using a fluorescence activated cell sorter, we have purified B-lineage cells into distinct populations based on their differential expression of cell surface markers. Clast6/E3/LAPTM5 was found to be highly expressed in progenitor and precursor B cells, downregulated in late pre-B and immature B cells, and upregulated again in mature B and the germinal center B cells. Interestingly, Clast6/E3/LAPTM5 was expressed at high levels in malignant B lymphomas. These results reveal stage-specific expression of Clast6/E3/LAPTM5 during B cell differentiation and implicates its possible involvement in B cell malignancies.