Class II transactivator (CIITA) is an effective transcriptional factor regulating various genes in the immune system. Since the detection of CIITA in 1993, there has been considerable progress toward understanding its role as an activator of MHC II genes in human and mouse; however, there is little knowledge of this gene in other animals such as chicken. Molecular characterization of the chicken CIITA gene transcript was performed to determine its sequence and expression in different tissues. The CIITA cDNA was first generated through reverse transcriptase-polymerase chain reaction (RT-PCR) from Cobb chicken spleen cell RNA, using oligonucleotide primers based on the predicted cDNA sequence. The effect of the immune system stimulation on the CIITA gene expression in kidney, liver, thymus, and spleen were assessed by semi-quantitative RT-PCR analysis. A partial cDNA sequence (1,688 bp) encoding part of the NACHT domain followed by seven of the transactivator and one of the NLS domains were obtained. Comparison of the deduced amino acid sequence with other CIITAs reveals high level of similarities in amino acid composition, secondary structure and phosphorylation sites. Furthermore, in comparison to the Red Jungle Fowl (RJF) sequence, we found 17 single nucleotide polymorphisms in Cobb broiler chicken, ten of which were reported for the first time. Gene expression analysis indicated that CIITA RNA amounts increased in all the examined tissues following stimulation with Brucella antigen. This investigation may indicate that CIITA molecule has an important role in the chicken immune responses as well as human and other animals.