Analysis of subclass-specific germline transcription in activated peripheral B cells revealed a highly biased expression pattern of the four Iγ transcripts to signals through CD40 and IL-4. This difference was most pronounced when comparing the profile of Iγ1 and Iγ4 transcripts and was not expected given the very high degree of sequence conservation between promoters. In this report, the influence of sequence differences on the regulation of the Iγ1 and Iγ4 promoters has been investigated given the highly muted transcriptional activity of the Iγ4 promoter. Two regions were analyzed where single nucleotide differences corresponded to major changes in transcriptional activity. These regions were the previously defined CD40 response region containing three putative NF-κB-binding sites and the downstream 36-bp region containing CREB/activating transcription factor and κB6 sites. Mutation of a single nucleotide at position 6 within the Iγ4 κB6 site increased promoter activity to ∼50% of the activity of the Iγ1 promoter. Furthermore, elevated promoter strength corresponded with increased binding of p50, p65, c-Rel, RelB, and p300 proteins to a level comparable with that of Iγ1. Minor nucleotide changes to both the Iγ4 CD40 response region and the 36-bp element resulted in a response undistinguishable from an Iγ1 response, suggesting cooperation between the two regulatory regions for optimal transcriptional activity. Collectively, these mutational analyses suggest that minor sequence differences contribute to the composition and affinity of transcriptional protein complexes regulating subclass-specific germline transcription, which in part impacts the overall level of class switch recombination to targeted CH regions.