HLA-DO, encoded by the HLA-DOA and HLA-DOB genes, has been shown to function as a modulator of Ag presentation. DNA microarray comparisons between B cells wild-type and mutant for the master regulator of MHC class II transcription, class II transactivator (CIITA), identified HLA-DOA and HLA-DOB as being up-regulated by CIITA. Although HLA-DOA had been shown previously to be regulated by CIITA, HLA-DOB expression was suggested to be independent of CIITA. A series of assays including quantitative RT-PCR, promoter-reporter assays, chromatin immunoprecipitations, and intracellular staining were performed to corroborate the DNA microarray analysis. The combined data demonstrate that HLA-DOB levels are increased by CIITA, and that this difference has an impact on the overall level of HLA-DO expression. Additionally, unlike the classical MHC class II genes, HLA-DOB expression was present in the absence of CIITA, indicating that additional factors mediate HLA-DOB expression in B cells.