The levels and stability of IκBε have been examined in unstimulated and stimulated splenic B cells and compared with that of IκBα and IκBβ. Primary murine splenic B cells but not T cells were found to contain high levels of IκBε protein, equivalent to levels of the abundant IκBα. Most agents that activate IκBα and IκBβ degradation do not induce rapid degradation of IκBε. Interestingly, however, the levels of IκBε, but not of IκBα or IκBβ, are dramatically reduced upon the stimulation of B cells both in vivo and in vitro. Since IκBε exhibits substrate specificity for NF-κB Rel homodimers, this suggested the possibility that changes in NF-κB-responsive genes might also occur during this transition. Consistent with this hypothesis, we found that a NF-κB reporter construct sensitive to p65/RelA homodimers is activated at the time that IκBε levels decline following B cell stimulation. In IgG+ B cell lines, which contain low levels of IκBε, this same reporter construct was inactive, suggesting that the increases in Rel homodimer activity that accompany B cell stimulation are transient. However, there are differences in the level of expression of NF-κB-responsive genes in these IgG+ B cell lines compared with their IgM+ counterparts. From these data, we conclude that there are transient changes in NF-κB activity due to reductions in IκBε, which might contribute to long-term, persistent changes that accompany B cell differentiation. We propose an important role for IκBε in the differential regulation of nuclear NF-κB activity in stimulated B cells.