MHC class II immuno-deficiency is a rare autosomal recessive disease due to a defect in transacting genes, which control the expression of the entire family of MHC alpha and beta class II genes. Previous analyses classified cells from eight MHC class II-deficient patients and four experimental mutant cell lines into four complementation groups, pointing to the existence of a large number of regulatory genes. We conducted fusion experiments with cell lines from two-thirds of all known patients and found that two complementation groups accounted for 20 of the 22 cases studied. These two complementation groups correspond closely to two ethnic groups: most patients of north African origin were classified into one group, while all patients originating from Spain were classified into a second main group. This suggests the existence of restricted number of ancestor mutations leading to this disease.