The MHC class II transactivator (CIITA) is the master regulator for HLA-D (DP, DQ, DR) The MHC class II transactivator (CIITA), a transcriptional co-activator, is the key intermediate responsible for IFN␥-inducible and constitutive class II expression on antigen presenting cells (APC). 1 CIITA also directs expression of invariant chain (Ii) and HLA-DM, 2 two molecules involved in class II biosynthesis and antigen processing. 3 Thus, CIITA is considered a global regulator of genes involved in class II-restricted Ag presentation. 2 The human CIITA gene, MHC2TA, which spans 42 kb, 4 was mapped to chromosome 16p13, 1 a region linked to multiple sclerosis (MS) susceptibility. 5,6 Given its pivotal role in MHC class II regulation, MHC2TA is also considered an important candidate gene in other autoimmune diseases. 7 In order to investigate the potential association of MHC2TA with autoimmune diseases, we have first examined the coding region and promoter elements in normal individuals for polymorphisms and established the allele frequencies of identified SNPs.The MHC2TA coding region from 50 unrelated Caucasian (non-Hispanic whites) individuals of northern European descent was examined for polymorphisms by bidirectional sequencing of lymphocyte cDNAs. Four SNPs were identified and were confirmed by sequencing gen-