In this study we analyzed fibroblasts derived from an MHC class II deficiency patient (type III bare lymphocyte syndrome). Northern blot analysis showed that upon induction with IFN-gamma these fibroblasts did not express HLA class II genes and displayed a strongly reduced level of HLA class I gene expression when compared with fibroblasts of a healthy individual. However, when analyzed by RT-polymerase chain reaction (PCR), residual expression could be detected for HLA-DRA, DPB, and DQA, but not for HLA-DRB, DPA, and DQB. The lack of HLA-DRB transcripts in the patient fibroblasts and the high degree of sequence polymorphism of HLA-DRB were exploited in the further analysis of these fibroblasts. Thus far, at least three, and probably four, complementation groups have been defined among patient-derived and experimentally-derived MHC class II-negative cell lines. Transient heterokaryons between the patient fibroblasts and representative B-lymphoblastoid cell lines from each of the complementation groups were analyzed by RT-PCR and Southern blotting, using HLA-DRB-specific primers and biotin-labeled sequence specific oligonucleotides, respectively. These analyses showed that the fibroblasts of this particular patient belonged to a novel complementation group in MHC class II deficiency.