CD40 is an integral plasma membrane-associated member of the TNF receptor family that has been recently shown to also reside in the nucleus of both normal B cells and Large B cell Lymphoma (LBCL) cells. However, the physiological function of CD40 in the B cell nucleus has not been examined. In this study, we demonstrate that nuclear CD40 interacts with the NF-kappaB protein-c-Rel, but not p65, in LBCL cells. Nuclear CD40 forms complexes with c-Rel on the promoters of NF-kappaB target genes-CD154, BLyS/BAFF and Bfl-1/A1 in various LBCL cell lines. Wild type CD40, but not NLS-mutated CD40, further enhances c-Rel mediated Blys promoter activation as well as proliferation in LBCL cells. Studies in normal B cells and LBCL patient cells further support a nuclear transcriptional function for CD40 and c-Rel. Cooperation between nuclear CD40 and c-Rel appears to be important in regulating cell growth and survival genes involved in lymphoma cell proliferation and survival mechanisms. Modulating the nuclear function of CD40 and c-Rel could reveal new mechanisms in LBCL pathophysiology and provide potential new targets for lymphoma therapy.