T-cell-dependent antigen induces differentiation of germinal center (GC) B-cell in peripheral lymphoid follicles. We studied whether GC B-cell differentiation is associated with DNA methylation status by examining regulatory regions of mouse AID transcription that are essential for B-cell maturation. AID-negative cell lines of pre-B cells, immature B cells, mature B cells, plasmacytomas or T cells showed various hypermethylation profiles in the 5′-promoter and intronic regions. In contrast, AID-positive GC-type B cells were hypomethylated in these regions. Stimulation of splenic B cells with lipopolysaccharide and interleukin-4 caused DNA hypomethylation in the 5′-promoter and intronic CpG sites proportional to the increase in AID transcription. Mature GL7+Fas+ GC B cells were hypomethylated at these CpG sites, especially near the Pax5-consensus site and an intronic site. However, Syndecan-1+ plasma cells showed DNA hypermethylation, as seen in plasmacytomas. Methylation status of the transcriptional regulatory region might contribute to stage-dependent activation of AID transcription during GC B-cell differentiation.