Types II and III bare lymphocyte syndrome (BLS) are severe or lethal congenital immunodeficiencies characterized by defective cell surface expression of HLA class II antigens. We have analyzed by Southern and Northern blotting B-lymphoblastoid cell lines derived by Epstein-Barr virus (EBV) transformation from peripheral blood lymphocytes of two unrelated BLS patients and their families. While DNA analyses of both families showed no indication of rearrangement or alteration of HLA region genes, class II mRNAs were virtually absent in the patients' cell lines (BLS-1 and BLS-2). This is consistent with previous observations of different BLS patients and their families. An exception to the absence of class II mRNAs in BLS was the detection of low quantities of HLA-DQ alpha transcripts in the cell lines BLS-1. This finding provides further evidence that factors regulating HLA-DQ expression may differ from those governing expression of the other class II genes.