Common variable immunodeficiency (CVI) is a heterogeneous condition characterized by arrest in B cell differentiation. A high frequency of null alleles of the C4 gene has been reported in patients with this disorder. We investigated the restriction fragment length polymorphisms (RFLP) of the MHC class II genes HLA-DRB, DQA, and DQB, the class III gene C4 and the tumour necrosis factor-alpha) (TNF-alpha) gene in 40 Caucasian patients. The results showed an increase in HLA-DR3 in patients (40% vs 30.5%), but, more significantly, there was a striking increase in the number of CVI patients who carried a deletion of the C4A gene (46% vs 25%). In both patients and controls there was strong allelic association between HLA-DR3 and C4A deletion, and HLA-DR3 and TNF-alpha. Our results suggest that genes present on an extended haplotype containing these three polymorphisms contribute to genetic susceptibility to CVI.