MHC (called HLA in man) class II genes play an essential role in cell-mediated immunity. Absence of HLA class II Ag on B lymphocytes is the basis of some congenital immunodeficiencies (CID). We have studied CID by generating transient heterokaryons from cell lines of such patients, and we report that the mutations fall into four complementation groups. In addition, fusions with the HLA class II deletion mutant 721.180 indicate that the genetic defects for each group in HLA class II expression map outside the HLA class II region. A small HLA-DRA promoter fragment is sufficient to drive expression of a reporter gene in normal B cell lines, but expression from the same construct is clearly reduced in mutant cell lines representative of all four complementation groups. This confirms earlier results that indicate defective transcription of HLA class II genes in the class II- CID mutant cell lines. Analysis of proteins that bind to the DRA promoter in nuclear extracts of the mutants suggests that complexes recognizing distinct elements of the DRA promoter may be quantitatively decreased in different mutants. In addition, we show that nuclear extracts from two groups fail to transcribe a DRA promoter construct in vitro accurately reflecting their DRA- phenotypes. In contrast, nuclear extracts from another mutant, RJ2.2.5, transcribe the DRA construct, albeit at a reduced level. Finally, though cell lines from different groups complement each other in vivo, no complementation was observed by mixing extracts for transcription in vitro.